Are there any common reasons why upgrading a database from SQL Server 2000 to SQL Server 2005 would result in slower queries? This is coming from an ASP.NET 1.1 application with hundred of tables, everything is indexed and seems to run well on the older version.
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We just experienced this issue after upgrade from 2000 Ent SP4 to 2005 Std 64 bit SP2, a much more powerful server too (2 4-core, 32GB RAM)
SELECT query took 2~3 secs on 2000 and 20+ minutes (and still not finished) on 2005 Re-built ALL indexes, sp_updatestats, same results. Very strange, no index hints were used except NOLOCK The databases remained in 8.0 compatible mode on the 2005 box though
Restoring to another 2005 box as we speak to test
Make sure that the queries and stored procedures you're running are not utilizing any index hints. Like everyone else has mentioned, the optimizer has changed between 2000 and 2005, so these hints may no longer be useful.