Since someone asked, yeah, when we decide on a date I'll ask people to sign up by posting their battle.net ID. At some sign-up cut-off, I'll take those signed up and put them in a bracket generator, post bracket. On the day of we'll have a check-in time, either via a website or logging into an IRC channel etc., something (Krassus offered a voice chat server). You friend the person you're playing, play your games, winner reports back. A lot of it is on you to find your opponent, be signed in, etc. Repeat till finals.
Edited that into the original post. This is basically how most HS tournaments work right now. Teamliquid's site has all their brackets/check-in stuff built-in, as does MLG, and most of the other small tournaments just use websites that have bracket/check-in functions. So if you want to play HS competitively this is what you'll be doing a lot.