Sharon Bjeletich has a post on SQLCAT about a SQL Server 2005\2008 Performance and Scalability Troubleshooting flowchart. The first step in the troubleshooting effort is to gain some background knowledge by reading the articles below (which I have helpfully linked to).
Troubleshooting Performance Problems in SQL Server 2005 (this is the best of the bunch)
HOW TO: Troubleshoot Application Performance with SQL Server (this is a little old)
How to troubleshoot slow-running queries on SQL Server 7.0 or on later versions (this is a little older)