Joan Strassman has a nice post at Sociobiology about how to choose a PhD program. I agree with most but not all of what she has to say.
I don’t agree that you just avoid M.Sc. programs if you think you might want a PhD. Unless you’re sure you want a PhD, doing an MSc is a good way to hedge your bets. It’s a much smaller commitment, both on your part and on the part of your advisor. If you’re unsure exactly what you want to work on, an M.Sc. can be a good way to find out, and gives you a natural way to change directions as your interests evolve. Lots of people do an M.Sc. in one lab and a Ph.D. on a somewhat different topic in another lab. But to do this you have to start, and finish, your M.Sc. first. If you start a Ph.D. and then for whatever reason decide you don’t want to finish it, you can often take an M.Sc. instead, but that’s colloquially known as a “terminal” M.Sc. If you do that, you’ll typically have a very hard time convincing anyone to take you on for a Ph.D. After all, you already tried and failed to finish one Ph.D.–why should anyone think you’ll succeed on your second try, or choose you over a competing applicant who hasn’t failed to finish? You may not think that’s fair, but that’s the reality.
There are other reasons to do an M.Sc. first. You’ll get a paper or two out of your M.Sc. thesis, which will make your CV stronger when you eventually finish grad school and enter the academic job market. Doing an M.Sc. and then a Ph.D. does extend your total time in grad school, but often not by much because you get all your coursework out of the way during your M.Sc. An M.Sc. also can qualify you for various jobs (e.g., certain environmental consulting positions, some technician/lab manager positions) for which a bachelor’s would not qualify you, so it’s not as if you’ve wasted your time if you end up deciding not to go for a Ph.D. And as for funding, while some universities don’t provide funding for their M.Sc. students, many do.
Note that I’m not saying you should do an M.Sc. to find out if you want to go to grad school at all. You should do your homework and figure that out before you start applying to graduate programs. You should be doing an independent study or honors research project, taking research assistant positions, and talking to your TAs to find out what doing research, and graduate school, is like.
UPDATE: Zen Faulkes has a nice post on why grad students fail. Many of these pitfalls can be avoided by doing your homework, and honestly assessing your own background and motivations, before you start applying.
Other advice I’d add:
Choosing the right advisor is more important than choosing the right program. I went to Rutgers because I wanted to work with Peter Morin, even though the Rutgers EEB program wasn’t on any lists of the top graduate programs in EEB. I’ve never regretted the choice. Don’t get me wrong, it’s fun and stimulating to be part of a top graduate program because you have the opportunity to interact with so many really good faculty and students. But your relationship with your supervisor is going to be much more important to your grad school experience. If you get on well with your supervisor and your labmates, you’ll have a good experience in grad school. If not, not. And once you leave, who your supervisor was counts for more than which program granted you your degree. When I was looking for jobs, I wasn’t viewed as a Rutgers graduate–I was viewed as a Morin lab graduate.
The exception to the above is that you definitely do not want to do your PhD at the same university where you got your bachelor’s (and your MSc, if you got one). If you don’t leave the nest, people will assume you can’t fly. Getting a bachelor’s in one place and both your graduate degrees somewhere else is fine. And getting a bachelor’s and master’s in one place and a Ph.D. someplace else is fine too. But getting your Ph.D. and all your pre-Ph.D. degrees in one place looks bad, even if you do different degrees under different advisors.
Here’s some advice I really can’t emphasize enough, because it concerns a really common mistake prospective grad students make. Before you contact any prospective advisor (at least in N. America), do your homework. Have a good look at their website, and read a couple of their papers. Then write each prospective advisor a personal email which is addressed specifically to that person and only to that person. Describe your background, interests, and long-term (i.e. post-grad school) goals, and say specifically why you want to join their lab (which doesn’t mean having a specific project in mind, of course). If you don’t do that, you’ve already gotten off on the wrong foot, and with many supervisors (including me) you’re already pretty much doomed. Most every decent advisor is very busy, and receives many, many inquiries from prospective students, many of them obviously bulk emails (many but not all of which come from students in developing countries). Every professor I know deletes such emails without reading them. If you can’t be bothered to take the time to do your homework before contacting me, why should I take the time to reply to you? Rather than signaling that you’re seriously interested in my lab, you’ve just signaled to me that you’re the kind of student who likes to cut corners and who doesn’t show initiative. Plus, if you don’t do your homework before contacting me, I’m just going to reply by asking you about your background, interests, long-term goals, and what specifically interests you about my lab. I mean, how else am I supposed to reply? So why not just save us both some time and send me a detailed, personal email to start with?
And then once you’ve corresponded with a few prospective advisors and narrowed the field to a few top choices, make sure to visit those labs before you make your final decision, and ideally before admission decisions are even made. Besides meeting your prospective advisor, you’ll get to meet their current grad students, see the facilities, and check out the city and the surrounding area. I actually insist on meeting prospective students face to face, with rare exceptions for students who are highly recommended by close colleagues whose judgment I trust. And no, skype or a phone call isn’t really a substitute. Most prospective advisors will at least encourage a visit even if they don’t insist on it, and will be happy to pay for it. Both you and your prospective advisor are considering making a big commitment to each other. It’s to the advantage of both of you to be as sure as possible that you’re a good match.