This is a very open ended question and there could be a lot of reasons behind the poor performance of a query. But some general issues that you could talk about would be:
Missing or out of date statistics,
Excess recompilations of stored procedures,
Procedures and triggers without SET NOCOUNT ON,
Poorly written query with unnecessarily complicated joins,
Too much normalization,
Excess usage of cursors and temporary tables.
Some of the tools/ways that help you troubleshooting performance problems are:
SET SHOWPLAN_ALL ON,
SET SHOWPLAN_TEXT ON,
SET STATISTICS IO ON,
SQL Server Profiler,
Windows NT /2000 Performance monitor,
Graphical execution plan in Query Analyzer.
Download the white paper on performance tuning SQL Server from Microsoft web site.