How can I write windowing query which sums a column to create discrete buckets?
I am not sure what type of performance you are looking for, but if CLR or external app is not an option, a cursor is all that is left. On my aged laptop I get through 1,000,000 rows in about 100 seconds using the following solution. The nice thing about it is that it scales linearly, so I would be looking at a little about 20 minutes to run through the entire thing. With a decent server you will be faster, but not an order of magnitude, so it would still take several minutes to complete this. If this is a one off process, you probably can afford the slowness. If you need to run this as a report or similar regularly, you might want to store the values in the same table un update them as new rows get added, e.g. in a trigger.

Anyway, here is the code:

IF OBJECT_ID('dbo.MyTable') IS NOT NULL DROP TABLE dbo.MyTable;

CREATE TABLE dbo.MyTable(
 Id INT IDENTITY(1,1) PRIMARY KEY CLUSTERED,
 v NUMERIC(5,3) DEFAULT ABS(CHECKSUM(NEWID())%100)/100.0
);


MERGE dbo.MyTable T
USING (SELECT TOP(1000000) 1 X FROM sys.system_internals_partition_columns A,sys.system_internals_partition_columns B,sys.system_internals_partition_columns C,sys.system_internals_partition_columns D)X
ON(1=0)
WHEN NOT MATCHED THEN
INSERT DEFAULT VALUES;

--SELECT * FROM dbo.MyTable

DECLARE @st DATETIME2 = SYSUTCDATETIME();
DECLARE cur CURSOR FAST_FORWARD FOR
  SELECT Id,v FROM dbo.MyTable
  ORDER BY Id;

DECLARE @id INT;
DECLARE @v NUMERIC(5,3);
DECLARE @running_total NUMERIC(6,3) = 0;
DECLARE @bucket INT = 1;

CREATE TABLE #t(
 id INT PRIMARY KEY CLUSTERED,
 v NUMERIC(5,3),
 bucket INT,
 running_total NUMERIC(6,3)
);

OPEN cur;
WHILE(1=1)
BEGIN
  FETCH NEXT FROM cur INTO @id,@v;
  IF(@@FETCH_STATUS &lt;&gt; 0) BREAK;
  IF(@running_total + @v &gt; 1)
  BEGIN
    SET @running_total = 0;
    SET @bucket += 1;
  END;
  SET @running_total += @v;
  INSERT INTO #t(id,v,bucket,running_total)
  VALUES(@id,@v,@bucket, @running_total);
END;
CLOSE cur;
DEALLOCATE cur;
SELECT DATEDIFF(SECOND,@st,SYSUTCDATETIME());
SELECT * FROM #t;

GO 
DROP TABLE #t;


It drops and recreates the table MyTable, fills it with 1000000 rows and then goes to work.

The cursor copies each row into a temp table while running the calculations. At the end the select returns the calculated results. You might be a little faster if you don't copy the data around but do an in-place update instead.

If you have an option to upgrade to SQL 2012 you can look at the new window-spool supported moving window aggregates, that should give you better performance. 

On a side note, if you have an assembly installed with permission_set=safe, you can do more bad stuff to a server with standard T-SQL than with the assembly, so I would keep working on removing that barrier - You have a good use case here where CLR really would help you.