I have been commishing leagues for many many years. In fact, the first year I ever played fantasy football I was a co-commissioner with another guy who had been playing for years. Needless to say, I saw many ups and downs the first two seasons.
General/Rules:
1 - My advice, if you run a league yourself, make sure your rules are absolutely clear so that everyone understands them and agrees to them before you even start the draft. Make sure that everyone has a hard copy of the rules. Make sure that you physically hand each owner a paper copy yourself. That paper copy is the official rules, not what the website says, in case you entered scoring incorrectly, set the waiver wire wrong, or the trade deadline incorrectly. That paper copy is the law of the league.
2 - Make sure everyone pays the league fee before the draft. I know, these guys/gals are your friends, they'll pay... not always true. If they don't have the money to pay on draft day, make them request an extension from the league, or pay a late fee, or both. I also offer credit card payment through paypal.com as a payment type for the league if my buddies agree to pay the credit card fee (no sense in the league having to take it out of the prize money). Try to get owners to pay even earlier if possible.
3 - I am a firm believer that the rules need to be followed absolutely as written and that no rules should be changed mid-season. However, allow a clause in the rules that allows the commissioner to make minor changes to the rules to allow for clarification, fix obvious errors, or to make minor adjustments to the rules to allow compatibility with the website. I say this because, my second season my rules read that the division champ was the team with the best division record, not that it was the first tiebreaker. The rules also stated that absolutely no rules may be changed once the game has begun. So, a team with 2 less wins won the division... How embarrassing!
4 - Have a predraft party/get together a week or so before the draft. Go over the rules. Allow voting for some rules changes, not all. I suggest creating a few options to be voted on yourself. Everyone will be more satisfied with the league if they feel that they are a part of creating it. At this time: draw out of a hat for draft position, possibly draw divisions at random, create the schedule (
http://schedules.footballguys.com/).
5 - If doing a live in-person draft definitely get a draft board. Good prices:
http://commishkit.com/. If most of your league is guys, get a hot chick or your girlfriend or a buddy's girlfriend to be a draft girl. It's not a hard job and really keeps the draft moving if each owner can simply call out the player name and position from their chair while someone else puts the sticker on the draft board.
Scoring:
1 - Make it basic and simple. If you would like some basic rules, PM me.
2 - Passing is a good stat category to put up for vote. Commonly passing will score 4 points or 5 points for a TD and 1 point for every 20 or 25 yards. Simply group 4pt TD with 1pt/25 yds as one option and 5pt TD with 1pt/20yds as the other option.... Both options score almost identically overall, but everyone gets input.
3 - Try not to severely overvalue or undervalue any one position.
Payouts:
1 - In my league that I play with my buddies, I pay out as many different options as I can think of. Afterall, it is for fun, and these are your friends. We pay-out 1st-4th, weekly high score all the way through the superbowl, pick 'em champ (whoever picks the most correct fantasy game winners throughout the season), coaching efficiency (best ratio of points scored to best possible score or roster), and week 17 free for all (everyone ubmits a roster and highest score takes a chunk of change).
2 - I pay-out about 50% to the champ, about 25% to 2nd, less to 3rd, and money back to 4th place.
Website:
1 - Many websites have the pick 'em and coaching efficiency built in, some do not.
2 - If you keep the rules simple, I would suggest going with a free website manager: espn.com, fantasysports.aol.com, easports.com/fantasy, fleaflicker.com. I personally hate Yahoo!
3 - If you use more complicated rules, my favorite site is fanball.com. It is about half the price of sportsline.com. Last year fantasysports.aol.com was identical to fanball.com.
I'm sure I missed something. If you have any specific questions feel free to PM me.
Oh yes, one more thing. Trading... I am a very objective commish. I handle trade issues myself. All trades automatically process on the website when it is accepted, however, I, the commish, am the only one that can overturn a trade. In my experience, if you leave it to a league vote, many owners will vote against it simply because they do not want to see a division opponent improve their roster not because they think that the trade is actually unfair. It also takes way too long. Less owners will be actively looking to trade when it takes 2 or 3 days for a trade to go through. Owners get into their leagues mostly on Saturdays and Sundays. You can't make a deal in that little of time if you want it for the upcoming scoring period. More people like fantasy football over any other sport for the reason that it is only once a week, not every day like baseball, basketball, and hockey. Help keep it easy for your owners. Using this method for years, I simply go to the two owners that are involved in the trade and discuss it with the both of them if I do not think that the trade is in the best spirit of the game. Not once has there been an issue or argument about a trade going through for the 6 years that I have used this method. I simply ask each owner separately to tell me how their team will benefit their team. Generally, the first thing out of their mouth when the trade is absolutely lopsided is, "What if we take out player A and add player B instead... or if we leave out player A altogether..." In other words, they know its not fair and adjust the deal to make it fair themselves. Then, I simply modify their original trade and announce on the message board that the details of the trade were altered by the owners. Everyone is happy and nobody gets pissed off or embarrassed.