I know how Magic (and likely PTCG) can be run.
Preliminaries will be a number of rounds of the Modified Swiss format. (First round pairings are random. Afterward, pairings are based on players who are closest in their current standing who haven't played each other. I could run that.) Number of rounds depends on the number participating. (1-8: just do single elimination. 9-16: 4 rounds. 16-32: 5 rounds, though this is unlikely.) Top 8 players advance to the single-elimination finals, with tiebreakers being (in order) opponents' match win percentage, player's game win percentage, opponents' total game win percentage. (Matches being best of three.)
Format might have to be regulated though, as anything-goes formats tend to be best decided by a flip of a coin. (To paraphrase someone on magicthegathering.com, vintage/type 1 games of magic, which are generally anything goes with very few exceptions, come in 3 phases: the early game is the opening die roll, the midgame is the mulligan decision, and the endgame is the first player's first turn, where he'll do his best to fuck over his opponent's first play.)
I personally like restricted card pools anyways. Less to think about.
I would vote for Modified and Standard myself. (Modified is currently everything from Diamond/Pearl on based on my googling, which would be D/P, Mysterious Treasures, Secret Wonders, Great Encounters, Majestic Dawn, and Legends Awakened. And Stormfront if it comes out before we do this. Standard, starting this Friday, will be 10th Edition, Lorwyn, Morningtide, Shadowmoor, Eventide, and Shards of Alara. Conflux is legal as soon as it comes out, but that's not until next year.)
Also stuff I would do:
-MtG (of course)
-LandGrab
-PTCG
-A Genesis Sonic Game Race if we do it. Or GBA.
Stuff I might do but stuff might prevent me from doing it:
-MKDS (if I manage to get wifi at some point, currently unlikely)
-Pokemon D/P (see MKDS. If we could go over Shoddy Battle, I'd definitely be game.)
-Sonic 2 (Gens netplay has failed in the past though oddly I can do zsnes netplay as I found out once.)
-TF2 (I could probably play over Hamachi, but that's it. Goddamn firewall.)
Also I'd suggest playing Warmachine/Hordes online through the Vassal engine, but I'm betting I'm the only one here who plays Warmachine so I'll dismiss that. Though if anyone's interested I'd probably just stick to 500 points, random maps/rolling for terrain, and just using the Assassins scenario. Keep it easy.