<p>Stanford has stronger science departments, and a much, much stronger engineering program. There will also be more students who share your love of the sciences, and more who share both a love for the sciences and the humanities and social sciences. That said, you may find that you'd actually prefer a weaker program because that may mean less competition and possibly more admiration/attention from the faculty. Stanford faculty will, of course, also happily get to know you, have you work in their lab, talk about their research, offer extra help outside of class, etc. </p>
<p>The housing system is a HUGE difference. I personally like Stanford's housing system because I can choose who I want to live with and what kind of housing I want. It can be sad not to see your freshman year friends much sophomore year, etc., but it's also a chance to meet new people, which I like a lot. Both systems have advantages and disadvantages. The row houses at Stanford are pretty neat. It's physically laid out a bit like a fraternity or sorority, only it's open to all students. Some row houses have themes, most of them have their own chefs, and they range from about 20-60 students each. </p>
<p>I doubt there are any clubs offered at either school that wouldn't exist at the other. If you're at all interested in conservative politics, there's the option of taking advantage of the Hoover Institute as a resource. Stanford has great sports teams, which can be a lot of fun to watch. </p>
<p>You know what Palo Alto is like, and realize that it isn't <em>that</em> close to San Fran, the beach, etc. You can of course still go to those places, but most students don't. If you really want to get away from home that may be a reason to go to Yale instead, but I have a few friends here who grew up in Palo Alto (one in Stanford!) and they don't seem to mind at all. </p>
<p>Weather is a big deal. It may seem silly, but it can really effect your mood and the mood of those around you. It also restricts what activities are possible. Ultimate frisbee in the middle of the winter doesn't really work when there's a blizzard. </p>
<p>One thing you should know that might tip the scale towards Yale is that there isn't tons of political discussion at Stanford. There's some, and I'm sure much more between friends who like talking about politics, but it's possible that there's more of it at east coast schools. If you start a conversation, people will be able to carry on an intelligent conversation about politics, but you may have to be the one to start it.</p>