I'm at Berkeley EE. I know this isn't a surprise, but I'd definitely recommend Berkeley CS over Stanford EE.
Quals:
Stanford's EE qual pass rate is 50% (first time) and it is significantly tougher than Berkeley's CS quals....the average is here is something like 75%, and if you choose the right area, it's closer to 90%. Berkeley admits a much smaller class than Stanford...from my friends down in Palo Alto, you will feel a lot more stress that first summer if you choose to go there. And you spend more time studying for it your first year that you could be doing research...at least that's our take on it.
Startup stuff:
Business-wise, I'm a part of the MOT program, and it is fantastic for working with MBA students. I have several friends that compete in lots of business plan competitions and such. The old thinking was that Berkeley was more for "open source" type projects and Stanford was more "startup" oriented, but that has changed. Berkeley had a really bad Intellectual Property department for many years, but it's changed in the last 5 years to be equal to Stanford. You're still closer to Silicon Valley in Palo Alto if that's important to you though. But if you want to do a startup here, there are plenty of others you can work with.
Finances:
Berkeley EECS doesn't have a financial problem...we're almost self-sufficient from the UC system because of all the funding we get from outside. Actually, we have received permission to do a few things to raise more money that the University prevented us from doing, so we're going to have even more money in a few years. We are going to be expanding the department with more faculty in the coming years, we just finished a new building / fab, and are renovating our old building floor by floor.
Personality:
On a "fun" note, Berkeley CS department really is fun to be a part of. As a member of Berkeley EE, we've tried to work with Stanford EE to organize some events together, but they are generally unreceptive. A lot of Stanford EE grads are older and more family oriented...so if that's something you're interested in, you'll like it. But Berkeley has much more community.
Overall:
Why'd I choose Berkeley? The professors....all of the stuff I said doesn't matter if you don't like the faculty. So choose the place you feel more comfortable with, and where you can find an advisor you'll work well with for the next 5 years.
Good luck with your decision!