I was checking out one of my Drupal sites and noticed that the watchdog table is > 3GB. I have plenty of space but it seems a big. Are there any best practices in regards to maintaining this table? I have run and cleared the cache.
Make sure that cron is running, that should clean that out the watchdog table regularly.
Drupal has a setting that controls how many rows should be kept, which you can configure at:
Additionally, you should check what kind of logs you have in that table. Maybe a module or something is causing a lot of notices which are all logged there (And considerable slow down your site!)
You can of course simply truncate the table, but you should first figure out why it's not getting cleaned and what is filling it up like that. How many rows are there?