When I was deciding where to apply, a few factors went into it. The biggest for me was geography. My wife and I wanted to be relatively close to our parents, which meant somwehere in the western US. Fortunately for me, that aren't that many programs in the west, especially outside of California. Other things I looked at:
* Program Reputation--I got a feel for this by talking to people at my home program and poking around websites--fairly or unfairly, a program that has few US medical school graduates probably doesn't have as much of a reputation as a program that's mostly US grads.
* Program Setting--at a free-standing children's hospital or not? Are there experiences outside the main program site? (I wanted a program based at a big children's hospital but with rotations at a more community-oriented hospital.)
* Size of Program--At a little program, you tend to know your peers (and faculty) better, but there's less flexibility is someone is ill or needs time off for other reasons while at a bigger program, there's definitely more flexibility for things that come up. There may also be more resources devoted to the program at a larger program (e.g., more full time staff or money), but that varies a lot.
* Program Culture/Personality--Admitedlly, this is hard to judge from afar, but you can sometimes get a feet from what is on websites or by talking to people who interviewed at the program the year before. The program I ended up definitely has an "outdoorsy" personality among the residents which fit me well, and you could see a little of that in the materials that the program sent out to applicants before they interviewed.
* Fellowship Opportunities - I wanted a program where I felt like I would feel comfortable staying in the same place for fellowship in three years so that I could keep that option open. My wife was frankly a little tired of picking up and moving every few years, so having the option will be a great thing. You'll hear all sorts of thoughts on whether havingn a lot of fellows is a good thing or a bad thing, but for me, I think that fellows tend to spend more time teaching and are able to teach at a resident level better than many attendings, so I like having them around.
In any event, there are a lot of good programs out there. I ended up interviewing at 12 programs, and felt that I would have been happy at 8 of them (which were the 8 that I ended up ranking). And despite my best efforts to figure out which programs I'd like in advance, there were a couple I expected to love that I hated and a couple I didn't really expect to like that ended up in my top 5, so you never know. Good luck as you apply this year!