To come back of my promise of last Friday, here's is my suggestion on how poker tournaments could work.
Tournament creation First step is to create the tournament. The organizer sets a start date and time, and defines a few parameters (limit/pot limit/no limit; stakes seconds/move, max/min number of players). (S)he also has to define the number of chips a player starts with - the "buy in". I can imagine two variants: 1) players bring in their own chips (as is done now for the existing poker tables) and 2) tournament chips are not related to the total number of chips a player owns - you get a number of chips to play with, and they're gone afterwards. There should be some checks so that the combination of parameters are sane (stakes 5/10 with 10000 starting chips or stakes 500/1000 with 750 starting chips are not desirable parameter combinations)
Tournament signup There will be no advance signup. The table(s) ought to open for players a few (10?) minutes before the sceduled start of the tournament. Players should be seated before the tournament starts - or else they cannot participate.
Sitting out You cannot leave the table - once you're in, you have to continue playing.
Winning condition The winning condition is simple: last person to have a positive number of chips wins the tournament.
Blinds Blinds should be automatic, and there's no sitting out.
Stake increase Over time, when players get eliminated, the average number of chips/player will go up. Stakes (including blinds) should increase during the course of the tournament. To pull some numbers out of thin air: a 10% increase each time a player gets eliminated from the table, or if the button (dealer) has passed around the table twice, which ever comes first.
Timeouts Eliminating a player if (s)he timeouts is perhaps a bit harsh. However, keeping her/him in and having him/her timeout over and over again is very annoying of the other players. So I suggest the following. Once a player time outs, (s)he goes into "time out mode". A player in time out mode always puts in her/his blind (if (s)he is a blind); otherwise, as soon as it is her/his turn, (s)he folds. That way (s)he doesn't hold up the game, nor can (s)he win. Also, if a player times out, a button appears on his/her screen. Pushing the button brings her/hime out of timeout mode, and back into the game.
More tables If a tournament has 10 players or less, the tournament can be played on a single table. Otherwise, the tournament has to start on more than one table. As soon as 5 (or, in rare cases less) players are left at a table, they advance to the next round (keeping their current number of chips). Repeat until there's one table, with one winner left. Of course, another cut-off number could be picked as well (perhaps only the top 3 should advance).