The biggest Bugs that I have come across are:

The Guestbooks need major security upgrades (Preferably restricted to Logged In Users only)

Orca has some major problems with Ads from Google, and sometimes OpenX. (Orca will generate a blank page with Out-of-Memory errors)

If you "Enable New Gallery" in the admin area, then you can no longer select a photo from the list and have it display. (The caption appears, but the photos continue to rotate)