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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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You didn't say which edition you are running.
But if you just moved from a 2000 Standard or Enterprise edition to a 2005 Express edition; The Express edition only uses one processor. I jsut had this happen to me last week; one of my queries went from an already slow 1.5 seconds to 55 seconds! I ran the query plan, and the only difference was the parallel operations. Couldn't beleive the speed difference.
Also, if all else fails, there is a bug in the 2005 optimizer addressed in SP2 cumulative update 6 (and requires applying 2 traceflags).
After the upgrade first thing you need to do is update the statistics with full scan and rebuild the indexes or you will get suboptimal plans
Are you certain that all of your indexes survived the upgrade? Are there any differences in hardware? Have you used the SQL Profiler to determine which queries are running slower to try to track down the problem?
There could be a lot of things. Without specific query examples and other information I don't think anyone will be able to help much.
A few things...
If you are using server side cursors, be aware that there are some performance problems that can start to surface after upgrading from SQL Server 2000 to SQL Server 2005. If this is your situation, there are a couple of hotfixes that might help. Just search for SQL Server 2005 hotfixes and server side cursors.
Aside from that, always be sure to check db integrity after the upgrade, rebuild indexes and update stats.
You may want to re-evaluate your indexes by looking at the execution plans of your most-troublesome queries. The SQL 2005 query optimizer may be coming up with completely different execution plans.
You should also make sure you update statistics on your entire database.