The biggest "bug" I can think of is the whole Superfetch algorithm is way too aggressive. It's not technically a bug - it's likely working as designed, but it's also responsible for a lot of the performance complaints in Vista. Microsoft turned it way down in Windows 7, and could have pushed out a patch to Vista to do the same, but never did.
The other big bug is Windows Explorer will randomly hang and shit itself, but it does the same thing in Windows 7.
I guess the other bug is the 497 day bug, which kills the network stack after 497 days of uptime (for reasons much like the 49.7 day bug in Windows 95), forcing a reboot. I've actually hit that one in Vista - yes, my all time personal Windows uptime record is currently held by a Vista box.