Thank you! I was able to Reindex all the user tables that were above 30% fragmentation successfully within the maintenance window. This server is in high demand since it runs our Emergency Room application 24/7. It is very difficult for us to get a downtime window with the Physicians. That being said I have noticed a few issues...

Even after rebuilding all the indexes, each time the nightly online index reorg job kicks on, the users experience issues with the application. It's not a rebuild but a reorg. Also, the mdf files and the ldf files are located on the same drive. This drive is highly fragmented. I tried to defrag it once I finished the index rebuild but ran out of time as the users needed it. Im still trying to figure out if that could be what is causing their issues with the online reorg job kicking in.

Quick facts: SQL Server 2000, Windows Server 2003 32bit with 3.5 GB Ram. I have set SQL Server Memory Min = 1024 and Max 2.5 GB. Any ideas?