My first tournament is the one ongoing now.
I don't know if its been the best, but some seem to think its been fair.
The trick is trying to limit fires before you have to put them out, especially since putting out fires as a non-moderator tournament director is bloody impossible.
My second peace of advice? Make timetables but don't expect to stick to them. The summer gunboat was supposed to be well into the finals right now, and we're not in the second leg yet. Each fire eats time that you never have.
And my last brown nugget of wisdom regards publicity. Never ever let people forget about the tournament. Start signups now, you need N players, so get N+10 names. Let people know what the tournament is worth point wise and keep reminding them. Let people know how things are going, what you're doing behind the scenes, the more transparency, the more people know how hard you're working and the less you have to hear moaning. Figure out your rules early and don't be afraid to modify them up to the date the tournament starts, they're set in stone then.
I lied about it being the last piece of need-to-know: Technical wise, use gmail to set up groups. I can let you login to mine if you want to see what I mean. It is definitely the BEST way to contact players about their games. Once you do it, every phase takes 5 minutes, not 5 hours. Google docs is another great tool: tinyurl.com/gunboattournament
Running a tournament takes a large investment of time up front, and then a barrage of tiny ones after. It's not difficult if you have an eye for management, and the mods are excellent at helping you keep the stress level down.
I'm happy to help set this up, but I can't quarterback this one. I promised TGM I'd help keep the tournament site together, and I've not even touched it yet. Plus yebellz came up with an awesome method for making tournaments bigger, and I've ignored that too. So, I'm happy to help set up all the tools I use to make the summer tournament not a headache, but someone with more time is going to need to fill in all the blank slots on the page.