You've seen them live!? Whoa! I've been meaning to, but they never come near me. I've got them on my list of people I need to see live before I die. Puscifer's cool as well. As for A Perfect Circle, I think they're still a band, they just haven't put anything out in a long while. My favorite Tool songs are: The Grudge (just an overall amazing example of Tool), Ticks & Leeches (drums on this = insane, plus Maynard's screams make it all worth the while), Stinkfist (great song), H. (amazing song, and very emotional as well), Lateralus (a complete epic), Hush (kind-of cool in-your-face sort of 'screw you' song), Sober (everybody loves it), Crawl Away (great song), The Pot (this song is just perfect), and, well, most of their songs.
My favorite Tool album is definitely Lateralus, closely followed by Ænima, that by 10,000 Days, that by Undertow, that by Opiate, and that by 72826.