Hey Kevin,
In my continued efforts to figure out why my site runs so slowly, I was scanning through the database a bit and noticed something odd: the "rewrite_rules" option is absolutely *enormous*. That single option is nearly 700,000 characters - easily two orders of magnitude larger than the second largest. A quick code search revealed that the only thing touching this option (aside from the core, of course) is Role-Scoper.
I'm not sure if this option would naturally grow so large, but I Googled around a bit and was not able to find any similar issues, so I'm lead to believe that it's come from this plugin. If so, is there any way to cull it down a bit? I can't imagine that 700,000 characters of modrewrite rules being loaded and parsed for each pageload wouldn't have a HUGE impact on performance… :/
Note that I do already have "filter uploaded file attachements" disabled in the options.
Also, I'm still running v1.3.44 due to the comment bug reported here: http://agapetry.net/forum/role-scoper/new-conflict-with-relevanssi-1344-1350/page-1.