Auditing which tables get joined most often
I don't know if you can differentiate joins vs straight queries, but you can use index activity (what version of SQL Server, by the way?) to get an idea of your "hot" tables.  This query should get you started, I use it to identify heavily fragmented or heavily used indexes, but it should still get you there.  I don't think it will work with heaps that well, but you really shouldn't have many of those (or any) without a good reason.  

I've written this mostly myself but of course cribbed and borrowed bits and pieces from others work.  My thanks go out to everyone who has ever posted code to the internet.

/**
    Author: Jonathan Fite

    Index Analyzer

    Requires CONTROL permission in the database, VIEW DATABASE STATE and VIEW SERVER STATE

*/

/** Initialize Variables. 

    @DatabaseID - The database we want to examine, must be specified, but defaults to the current database...
    @IndexScanLevel - The level of detail you want to scan to.
        - LIMITED - This is the default or NULL value, only looks at the parent level of the index.  
        - SAMPLED - Detailed look at ~1% of the pages in the index. (Heaps and indexes smaller than 10K Pages use DETAILED)
        - DETAILED - full scan of all pages, heavy IO
    @MinFragmentation - If you want to see only indexes fragmented to a certain level.
    @MinPageCount - To limit to indexes that are over a certain page count.  Small indexes don't typically benefit
        from being defragmented.  A good number to start with is 100

*/

DECLARE @DatabaseID INT;
SET @DatabaseID = (SELECT DB_ID());

DECLARE @IndexScanLevel NVARCHAR(10);
SET @IndexScanLevel = 'SAMPLED';

DECLARE @MinFragmentation DECIMAL(4,2);
SET @MinFragmentation = 0.0;

DECLARE @MinPageCount INT;
SET @MinPageCount = 100;

/** Begin Work on the Query *********************************************************/

--Get Column List Information
DECLARE @ColumnList AS TABLE
    (
    object_id INT NOT NULL
    , index_id  INT NOT NULL
    , IndexedColumns VARCHAR(8000) NULL
    , IncludedColumns VARCHAR(8000) NULL
    );

WITH CTE_ColumnList AS
(
    SELECT IC.object_id
        , IC.index_id, C.name
        , IC.key_ordinal AS Position
        , DisplayName = C.name + CASE WHEN IC.is_descending_key = 1 THEN ' DESC' ELSE '' END
        , IC.is_included_column
    FROM sys.index_columns IC
        INNER JOIN sys.columns C ON C.object_id = IC.object_id AND IC.column_id = C.column_id
)
INSERT INTO @ColumnList
        ( object_id ,
          index_id ,
          IndexedColumns ,
          IncludedColumns
        )
SELECT DISTINCT 
    C.object_id
    , C.index_id
    , IndexedColumns = STUFF((SELECT ', ' + E.DisplayName FROM CTE_ColumnList E WHERE E.object_id = C.object_id AND E.index_id = C.index_id AND E.is_included_column = 0 ORDER BY E.Position FOR XML PATH('')), 1,1,'')
    , IncludedColumns  = STUFF((SELECT ', ' + E.DisplayName FROM CTE_ColumnList E WHERE E.object_id = C.object_id AND E.index_id = C.index_id AND E.is_included_column = 1 ORDER BY E.Position FOR XML PATH('')), 1,1,'')
FROM CTE_ColumnList C;

SELECT DB_NAME(IPS.database_id) AS DatabaseName
    , SchemaName = S.name
    , ObjectName = O.name
    , O.type_desc AS ObjectType
    , I.name AS IndexName
    , IPS.index_type_desc
    , IPS.alloc_unit_type_desc
    , IPS.avg_fragmentation_in_percent
    , IPS.avg_page_space_used_in_percent 
    , IPS.page_count
    , PageSize_MB = (IPS.page_count/128.0)
    , I.is_unique
    , I.fill_factor
    , I.is_disabled
    , I.has_filter
    , I.filter_definition
    , IUS.user_seeks
    , IUS.user_scans
    , IUS.user_lookups
    , IUS.user_updates
    , UsageActivityTotal = IUS.user_seeks + IUS.user_scans + IUS.user_lookups + IUS.user_updates
    , IOS.leaf_insert_count
    , IOS.leaf_update_count
    , IOS.leaf_delete_count
    , OperationalActivityTotal = IOS.leaf_insert_count + IOS.leaf_update_count + IOS.leaf_delete_count
    , LastAccessed = IUS_LastUsed.LastUsed
    , CL.IndexedColumns
    , CL.IncludedColumns
FROM sys.dm_db_index_physical_stats(@DatabaseID, NULL, NULL, NULL, @IndexScanLevel) AS IPS
    INNER JOIN sys.objects O ON O.object_id = IPS.object_id
    INNER JOIN sys.schemas S ON S.schema_id = O.schema_id
    INNER JOIN sys.indexes I ON I.object_id = IPS.object_id AND I.index_id = IPS.index_id
    LEFT OUTER JOIN @ColumnList CL ON CL.object_id = IPS.object_id AND CL.index_id = IPS.index_id
    LEFT OUTER JOIN sys.dm_db_index_usage_stats IUS ON IUS.database_id = IPS.database_id AND IUS.object_id = IPS.object_id AND IUS.index_id = IPS.index_id
    LEFT OUTER JOIN sys.dm_db_index_operational_stats(@DatabaseID, NULL, NULL, NULL) IOS ON IOS.object_id = IPS.object_id AND IOS.index_id = IPS.index_id
    LEFT OUTER JOIN (
                    SELECT S.database_id
                        , S.object_id
                        , S.index_id
                        , MAX(S.lastused) AS LastUsed
                    FROM sys.dm_db_index_usage_stats UNPIVOT (lastused FOR nlastused IN (last_user_seek, last_user_scan, last_user_lookup, last_user_update)) AS S
                    GROUP BY S.database_id
                        , S.object_id
                        , S.index_id
                    ) IUS_LastUsed ON IUS_LastUsed.database_id = IPS.database_id AND IUS_LastUsed.object_id = IPS.object_id AND IUS_LastUsed.index_id = IPS.index_id
WHERE ISNULL(O.is_ms_shipped, 0x0) = 0x0 --Exclude System Generated Objects
    AND ISNULL(I.is_disabled, 0x0) = 0x0 --Exclude Disabled Indexes
    AND ISNULL(IPS.page_count, 0) &gt;= @MinPageCount --Only worry about indexes with worthwhile page counts
    AND ISNULL(IPS.avg_fragmentation_in_percent, 0.0) &gt;= @MinFragmentation --Only display indexes that exceed fragmentation threshold
ORDER BY IPS.avg_fragmentation_in_percent DESC;