I hear alot of people saying good things about Things on the mac, haven't played with it in awhile. I use a crap load of filters in GMail to make my life sane, but I too am running into the "how do we keep track of all this stuff" when it comes to biz/app. Just started using Google Sites to at it wiki style. Debating on something like Pivotal Tracker but I dont think we're that organized yet. I hate introducing a tool/process/app that is more work than what problem its trying to resolve.
Deep down, can't beat a good moleskin these days really.