Why does DELETE leave a lingering effect on performance?
This difference only seems to apply when the object is a B+tree. When removing the primary key on the table variable so it is a heap I got the following results

2560
2120
2080
2130
2140


But with the PK I found a similar pattern in my tests as well with typical results below.

+--------+--------+---------+-------------------+
| @table | #table | ##table | [permanent_table] |
+--------+--------+---------+-------------------+
|   2670 |   2683 |    9603 |              9703 |
|   6823 |   6840 |    9723 |              9790 |
|   6813 |   6816 |    9626 |              9703 |
|   6883 |   6816 |    9600 |              9716 |
|   6840 |   6856 |    9610 |              9673 |
+--------+--------+---------+-------------------+


My theory is that there there is some optimisation available when doing bulk inserts to local temporary B+ trees that only applies when it does not already have any pages allocated. 

I base this on the following observations.


When running various versions of your test code I only saw this pattern  with @table_variables and #temp tables. Not permanent tables in tempdb nor ## tables.
In order to get the slower performance it is not necessary to have previously added and removed a large amount of rows from the table. Simply adding a single row and leaving it in there is sufficient.
TRUNCATE deallocates all pages from the table. DELETE will not cause the last page in the table to be deallocated. 
Using the VS 2012 profiler shows that in the faster case SQL Server uses a different code path. 36% of the time is spent in sqlmin.dll!RowsetBulk::InsertRow vs 61% of the time spent in sqlmin.dll!RowsetNewSS::InsertRow for the slower case.


Running 

SELECT * 
FROM sys.dm_db_index_physical_stats(2,OBJECT_ID('tempdb..#values'),1,NULL, 'DETAILED')


after the delete returns

+-------------+------------+--------------+--------------------+
| index_level | page_count | record_count | ghost_record_count |
+-------------+------------+--------------+--------------------+
|           0 |          1 |            0 |                  1 |
|           1 |          1 |            1 |                  0 |
|           2 |          1 |            1 |                  0 |
+-------------+------------+--------------+--------------------+


I found that it was possible to reduce the time discrepancy somewhat by enabling trace flag 610. 

This had the effect of reducing the quantity of logging substantially for the subsequent inserts (down from 350 MB to 103 MB as it no longer logs the individual inserted row values) but this had only a minor improvement in timings for the 2nd and subsequent @table , #table cases and the gap still remains. The trace flag improved the general performance of inserts to the other two table types significantly.

+--------+--------+---------+-------------------+
| @table | #table | ##table | [permanent_table] |
+--------+--------+---------+-------------------+
|   2663 |   2670 |    5403 |              5426 |
|   5390 |   5396 |    5410 |              5403 |
|   5373 |   5390 |    5410 |              5403 |
|   5393 |   5410 |    5406 |              5433 |
|   5386 |   5396 |    5390 |              5420 |
+--------+--------+---------+-------------------+


From looking in the transaction log I noticed that the initial inserts against empty local temporary tables seem even more minimally logged (at 96 MB).

Notably these faster inserts had only 657 transactions (LOP_BEGIN_XACT /LOP_COMMIT_XACT pairs) compared with over 10,000 in the slower cases. In particular LOP_FORMAT_PAGE operations seem much reduced. The slower cases have a transaction log entry for this for each page in the table (about 10,270) compared with only 4 such entries in the fast case.

The log used in all three cases was as follows (I have deleted the log records for updates to system base tables to reduce the amount of text but they are still included in the totals)

Logging first insert against @table_var (96.5 MB)

+-----------------------+----------+----------------------------------------------+---------------+---------+
|       Operation       | Context  |                AllocUnitName                 | Size in Bytes |   Cnt   |
+-----------------------+----------+----------------------------------------------+---------------+---------+
| LOP_BEGIN_XACT        | LCX_NULL | NULL                                         |         83876 |     658 |
| LOP_COMMIT_XACT       | LCX_NULL | NULL                                         |         34164 |     657 |
| LOP_CREATE_ALLOCCHAIN | LCX_NULL | NULL                                         |           120 |       3 |
| LOP_FORMAT_PAGE       | LCX_HEAP | dbo.#531856C7                                |            84 |       1 |
| LOP_FORMAT_PAGE       | LCX_IAM  | dbo.#4F47C5E3.PK__#4F47C5E__3213E83F51300E55 |            84 |       1 |
| LOP_FORMAT_PAGE       | LCX_IAM  | dbo.#531856C7                                |            84 |       1 |
| LOP_FORMAT_PAGE       | LCX_IAM  | Unknown Alloc Unit                           |            84 |       1 |
| LOP_HOBT_DDL          | LCX_NULL | NULL                                         |           216 |       6 |
| LOP_HOBT_DELTA        | LCX_NULL | NULL                                         |           320 |       5 |
| LOP_IDENT_NEWVAL      | LCX_NULL | NULL                                         |     100240000 | 2506000 |
| LOP_INSERT_ROWS       | LCX_HEAP | dbo.#531856C7                                |            72 |       1 |
| LOP_MODIFY_ROW        | LCX_IAM  | dbo.#531856C7                                |            88 |       1 |
| LOP_MODIFY_ROW        | LCX_PFS  | dbo.#4F47C5E3.PK__#4F47C5E__3213E83F51300E55 |        158592 |    1848 |
| LOP_MODIFY_ROW        | LCX_PFS  | dbo.#531856C7                                |            80 |       1 |
| LOP_MODIFY_ROW        | LCX_PFS  | Unknown Alloc Unit                           |        216016 |    2455 |
| LOP_SET_BITS          | LCX_GAM  | dbo.#4F47C5E3.PK__#4F47C5E__3213E83F51300E55 |         84360 |    1406 |
| LOP_SET_BITS          | LCX_GAM  | Unknown Alloc Unit                           |        147120 |    2452 |
| LOP_SET_BITS          | LCX_IAM  | dbo.#4F47C5E3.PK__#4F47C5E__3213E83F51300E55 |         84360 |    1406 |
| LOP_SET_BITS          | LCX_IAM  | Unknown Alloc Unit                           |        147120 |    2452 |
| Total                 | NULL     | NULL                                         |     101209792 | 2519475 |
+-----------------------+----------+----------------------------------------------+---------------+---------+


Logging subsequent inserts TF 610 off (350 MB)

+-----------------------+--------------------+----------------------------------------------+---------------+---------+
|       Operation       |      Context       |                AllocUnitName                 | Size in Bytes |   Cnt   |
+-----------------------+--------------------+----------------------------------------------+---------------+---------+
| LOP_BEGIN_CKPT        | LCX_NULL           | NULL                                         |            96 |       1 |
| LOP_BEGIN_XACT        | LCX_NULL           | NULL                                         |       1520696 |   12521 |
| LOP_COMMIT_XACT       | LCX_NULL           | NULL                                         |        651040 |   12520 |
| LOP_CREATE_ALLOCCHAIN | LCX_NULL           | NULL                                         |            40 |       1 |
| LOP_DELETE_SPLIT      | LCX_INDEX_INTERIOR | dbo.#4F47C5E3.PK__#4F47C5E__3213E83F51300E55 |          2160 |      36 |
| LOP_END_CKPT          | LCX_NULL           | NULL                                         |           136 |       1 |
| LOP_FORMAT_PAGE       | LCX_HEAP           | dbo.#4F47C5E3.PK__#4F47C5E__3213E83F51300E55 |        859236 |   10229 |
| LOP_FORMAT_PAGE       | LCX_IAM            | Unknown Alloc Unit                           |            84 |       1 |
| LOP_FORMAT_PAGE       | LCX_INDEX_INTERIOR | dbo.#4F47C5E3.PK__#4F47C5E__3213E83F51300E55 |          3108 |      37 |
| LOP_HOBT_DDL          | LCX_NULL           | NULL                                         |           648 |      18 |
| LOP_HOBT_DELTA        | LCX_NULL           | NULL                                         |        657088 |   10267 |
| LOP_IDENT_NEWVAL      | LCX_NULL           | NULL                                         |     100239960 | 2505999 |
| LOP_INSERT_ROWS       | LCX_CLUSTERED      | dbo.#4F47C5E3.PK__#4F47C5E__3213E83F51300E55 |     258628000 | 2506000 |
| LOP_INSERT_ROWS       | LCX_HEAP           | dbo.#531856C7                                |            72 |       1 |
| LOP_INSERT_ROWS       | LCX_INDEX_INTERIOR | dbo.#4F47C5E3.PK__#4F47C5E__3213E83F51300E55 |       1042776 |   10302 |
| LOP_MODIFY_HEADER     | LCX_HEAP           | dbo.#4F47C5E3.PK__#4F47C5E__3213E83F51300E55 |        859236 |   10229 |
| LOP_MODIFY_HEADER     | LCX_INDEX_INTERIOR | dbo.#4F47C5E3.PK__#4F47C5E__3213E83F51300E55 |          3192 |      38 |
| LOP_MODIFY_ROW        | LCX_IAM            | dbo.#4F47C5E3.PK__#4F47C5E__3213E83F51300E55 |           704 |       8 |
| LOP_MODIFY_ROW        | LCX_PFS            | dbo.#4F47C5E3.PK__#4F47C5E__3213E83F51300E55 |        934264 |   11550 |
| LOP_MODIFY_ROW        | LCX_PFS            | Unknown Alloc Unit                           |        783984 |    8909 |
| LOP_SET_BITS          | LCX_GAM            | dbo.#4F47C5E3.PK__#4F47C5E__3213E83F51300E55 |         76980 |    1283 |
| LOP_SET_BITS          | LCX_GAM            | Unknown Alloc Unit                           |        534480 |    8908 |
| LOP_SET_BITS          | LCX_IAM            | dbo.#4F47C5E3.PK__#4F47C5E__3213E83F51300E55 |         76980 |    1283 |
| LOP_SET_BITS          | LCX_IAM            | Unknown Alloc Unit                           |        534480 |    8908 |
| LOP_SHRINK_NOOP       | LCX_NULL           | NULL                                         |            32 |       1 |
| LOP_XACT_CKPT         | LCX_NULL           | NULL                                         |            92 |       1 |
| Total                 | NULL               | NULL                                         |     367438748 | 5119297 |
+-----------------------+--------------------+----------------------------------------------+---------------+---------+


Logging subsequent inserts TF 610 on (103 MB)

+-------------------------+-------------------------+----------------------------------------------+---------------+---------+
|        Operation        |         Context         |                AllocUnitName                 | Size in Bytes |   Cnt   |
+-------------------------+-------------------------+----------------------------------------------+---------------+---------+
| LOP_BEGIN_CKPT          | LCX_NULL                | NULL                                         |           192 |       2 |
| LOP_BEGIN_XACT          | LCX_NULL                | NULL                                         |       1339796 |   11099 |
| LOP_BULK_EXT_ALLOCATION | LCX_NULL                | NULL                                         |         20616 |     162 |
| LOP_COMMIT_XACT         | LCX_NULL                | NULL                                         |        577096 |   11098 |
| LOP_CREATE_ALLOCCHAIN   | LCX_NULL                | NULL                                         |            40 |       1 |
| LOP_DELETE_SPLIT        | LCX_INDEX_INTERIOR      | dbo.#6DCC4D03.PK__#6DCC4D0__3213E83F6FB49575 |          2160 |      36 |
| LOP_END_CKPT            | LCX_NULL                | NULL                                         |           272 |       2 |
| LOP_FORMAT_PAGE         | LCX_BULK_OPERATION_PAGE | dbo.#6DCC4D03.PK__#6DCC4D0__3213E83F6FB49575 |        863520 |   10280 |
| LOP_FORMAT_PAGE         | LCX_IAM                 | Unknown Alloc Unit                           |            84 |       1 |
| LOP_FORMAT_PAGE         | LCX_INDEX_INTERIOR      | dbo.#6DCC4D03.PK__#6DCC4D0__3213E83F6FB49575 |          3108 |      37 |
| LOP_HOBT_DELTA          | LCX_NULL                | NULL                                         |        666496 |   10414 |
| LOP_IDENT_NEWVAL        | LCX_NULL                | NULL                                         |     100239960 | 2505999 |
| LOP_INSERT_ROWS         | LCX_CLUSTERED           | dbo.#6DCC4D03.PK__#6DCC4D0__3213E83F6FB49575 |         23544 |     218 |
| LOP_INSERT_ROWS         | LCX_HEAP                | dbo.#719CDDE7                                |            72 |       1 |
| LOP_INSERT_ROWS         | LCX_INDEX_INTERIOR      | dbo.#6DCC4D03.PK__#6DCC4D0__3213E83F6FB49575 |       1042776 |   10302 |
| LOP_MODIFY_HEADER       | LCX_BULK_OPERATION_PAGE | dbo.#6DCC4D03.PK__#6DCC4D0__3213E83F6FB49575 |        780216 |   10266 |
| LOP_MODIFY_HEADER       | LCX_HEAP                | dbo.#6DCC4D03.PK__#6DCC4D0__3213E83F6FB49575 |       1718472 |   20458 |
| LOP_MODIFY_HEADER       | LCX_INDEX_INTERIOR      | dbo.#6DCC4D03.PK__#6DCC4D0__3213E83F6FB49575 |          3192 |      38 |
| LOP_MODIFY_ROW          | LCX_IAM                 | dbo.#6DCC4D03.PK__#6DCC4D0__3213E83F6FB49575 |           704 |       8 |
| LOP_MODIFY_ROW          | LCX_PFS                 | dbo.#6DCC4D03.PK__#6DCC4D0__3213E83F6FB49575 |        114832 |    1307 |
| LOP_MODIFY_ROW          | LCX_PFS                 | Unknown Alloc Unit                           |        231696 |    2633 |
| LOP_RANGE_INSERT        | LCX_NULL                | NULL                                         |            48 |       1 |
| LOP_SET_BITS            | LCX_GAM                 | dbo.#6DCC4D03.PK__#6DCC4D0__3213E83F6FB49575 |         77100 |    1285 |
| LOP_SET_BITS            | LCX_GAM                 | Unknown Alloc Unit                           |        157920 |    2632 |
| LOP_SET_BITS            | LCX_IAM                 | dbo.#6DCC4D03.PK__#6DCC4D0__3213E83F6FB49575 |         77100 |    1285 |
| LOP_SET_BITS            | LCX_IAM                 | Unknown Alloc Unit                           |        157920 |    2632 |
| LOP_XACT_CKPT           | LCX_NULL                | NULL                                         |            92 |       1 |
| Total                   | NULL                    | NULL                                         |     108102960 | 2602218 |
+-------------------------+-------------------------+----------------------------------------------+---------------+---------+