Pros
It's the undisputed leader in its industry, and is still enjoying healthy growth (including internationally) in spite of the weak economy. You'll have the satisfaction of working for a company with a strong reputation in a field (medical software) that directly benefits mankind. Some people enjoy the lax dress code and offbeat campus environment, and you may have opportunities to travel to hospitals in places like southern California or Hawaii (though it could just as easily be Idaho or South Dakota). The employees are generally young and bright, and Madison consistently ranks as one of the best places to live in the US.
Cons
Employees are treated like children. The company practices ageism in hiring (if you're over 30, don't even bother). There's a severe lack of experienced employees due to their too-rapid growth and constant turnover issues (largely due to travel-related stress and disgust with all the rah-rah corporate brainwashing). The campus seems nifty at first, but the forced quirkiness quickly gets irritating and then downright obnoxious. Due to the lack of a dress code, the employees dress like children or homeless people. Middle management is incompetent (promotions are largely based on who puts in the most hours). All real decisions are made by the top 10 or so senior managers, so unless you can get one of their jobs (you won't) there's no real upside for your career. You only get paid once a month. You will be thoroughly trained on your application, but not on your actual job responsibilities, so that when you actually start work you'll be expected to BS your way along until you figure out what's what. You will be pressured to "get with the program" and become an "Epic person" like it was some kind of cult, and Heaven help you if you get on Judy's bad side. The company is still basically being run like a startup with 100 employees rather than a major enterprise with 3000, leading to bottlenecks and all-around cluelessness. The company is also managed based on KLAS industry surveys, so a single bad review from a single disgruntled user can dramatically effect the whole organization's strategy. It's unlikely you'll actually have your own office for the next year or two until the new buildings are up, though they may tell you otherwise. The employees, while admittedly smart (though not as much as many of them seem to think), are mostly inexperienced and directionless Midwestern kids who just wound up here because they thought the place looked neat, not because they ever intended to work for a medical software company, so don't expect much ambition or drive from your co-workers (except for the true believers, there's always a few of them), and don't be surprised if half of your fellow new hires quit in the first eighteen months. And as for Madison, make sure you own a good parka, and be prepared for the 40k drunk college students clogging up all the downtown bars, parks, concerts, sidewalks, bike paths, apartment buildings, etc.