So I have an idea that I would like to have a storewide twilight imperium day like other games have tournaments. I really would like to use this as a vehicle to raise money for charity.

Question being: how would you guys recommend seeing it up? What prizes would be good?

Any suggestions or other thoughts are also welcome.

I'm not sure that TI3 is really the best choice of game for a tournament, to be honest. It's a long game to begin with, and adding a competitive tournament angle would slow things down as people try to optimize their game. You'll probably have high player counts (6-8 players per table) as well. This could EASILY make a single game fill out an entire 8-12 hour working day for the store, and having only one round of play limits the effectiveness of a tournament.

If you want this to work, I think the first thing you need to do is come up with house rules and/or prebuilt maps that will help limit play time to something reasonable (3-4 hours per tournament round, ideally.)

Maybe you can limit each table to 3-4 players, which would also help with round robin play styles and player elimination schedules, although even so I expect it will be a LONG day.

As for prizes, perhaps giving away one or more of the copies of the game used to play the tournament?

Another option, possibly, would be to limit the time of each game to, say, 4 hours and the one or two player(s) with the most points advances to the next round. If more than 2 players are tied for most one could go for some form of sudden death. The Accelerated Setup option would probably be useful in such a case. And artifacts would make for more points to compete over.

Not sure how feasable it would be but that's from the top of my head.

I really wasn't thinking a multiple game per day tournament. I was more on the line of thinking that it would be like the lotr fellowship events. Just get a big gaggle of players separate them into games of 4-6. Therm have some raffle prizes door prizes and prizes for the winner.

Could make it a marathon type thing like the extra-life charity thing. Set the games up with all the optional rules (including long war) and the challenge is to actually last until the end. Divide the players up into as few games as possible so all the games are 6-8 players and get people to sponsor players based on how long they last.