As sports, I prefer football to baseball, largely because of the reasons chad stated. There are more variables that come into play in a football game. Everyone has to be on the same page and everything has to go right for a play to work.
As fantasy, I prefer baseball slightly over football. Most fantasy players, myself included, love stats. There are far more stats in baseball than there are in football. You can basically look at 2 stats in football to tell their value. Yards and TDs. In baseball, you can have a guy hit 40 HRs and have 110 RBIs, but his BA could suck. You can have a guy have 120 Rs and 50 SBs, but his HRs and RBI numbers could be horrible. There are different types of players at the various different positions. While the same is true for football, it's not even close to the extent that it is at baseball.
Rosters are much larger in baseball and that is another reason why it can be more fun than football. More players to watch. There are 162 games in baseball as opposed to only 17 in football. More games to watch.
However, these people that claim football is a joke compared to baseball because of the 17 games compared to 162 games apparently haven't been caught up to speed on the differences of the game. News Flash: Football is a contact sport. Baseball is not. There is a reason why football players get a week's rest between games and baseball players play every day. Football is more physically taxing. I love baseball, but there are far too many players who take it easy during games and treat it like a job instead of a sport. In football, you'd be killed if you did that. It's 100% all the time in football (unless you're Randy Moss). It's only 100% in baseball when you're a pitcher, you're a baserunner like Sizemore or Freel, you're stealing a base, or you're an outfielder running down a fly ball. There are other examples I know, but the fact that I can actually categorically put them down speaks volumes for the differences. You can't do that with football. As soon as that ball is snapped there's no jogging. That's why I prefer football, as a sport, over baseball.
Don't tell anyone on the LightSide what I said about liking fantasy baseball more than fantasy football.