Well, if there is a "long running query" and I need to find the reason for "why" it is running so long, I proceed like this:

1. Run SQL Profiler; searching for queries which have a high number of "Reads". This mostly indicates "Index Scans" which could cause the long runtime. Check the "Execution PLan" of those queries to optimize e.g. Indexes etc.. According to this you should check the Statistics and Fragmentation degree of that table and fix it if necessary

2. Checking for Blocks. I proceed as described here: http://dynamicsuser.net/blogs/stryk/archive/2008/11/03/blocks-amp-deadlocks-in-nav-with-sql-server.aspx

3. Check "Wait Statistics" to find out if theres an I/O problem, e.g. a problem with network or disk-subsystem. Therefore I look into the "sys.dm_os_wait_stats" DMV