I'd also vote for Philz Coffee towards the north end of Berkeley, I've worked out of there whenever I'm not meeting down @ YC in mountain view. The coffee is fuel for me (other than cheesily being motivated by happy tweets from fanvibe users =)

If it's a late night gathering, I love going to the Pub in Albany/North Berkeley. Awesome atmosphere, awesome belgian beers. Pretty cool people there too. it's well lit, no music, so it's easy to talk and hang out in.