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I'm in the lucky position of having two PhD offers, both in structural biology, one at Oxford (Wellcome Trust, 4 years funding) and the other at Cambridge (MRC-LMB, 3 years funding although slightly less per year) but I just cannot decide which to go for. I have been an undergraduate at Oxford for the past 4 years. Does anyone have any opinions or advice about making my decision, things to consider etc.?

Maybe you should base your decision on how well you get on with your potential supervisors and which project appeals to you more?

first of all, what a nice choice to have, lucky you!
secondly, i agree with melsie, how well you get on with your supervisors is vital to how well you will do in your phd! go with your gut instinct as to which project really feels 'right' for you.
as i understand it, the wellcome trust phd's include a year of taught classes at the beginning, kind of like a masters, which is why they are funded for 4 years instead of 3. so do you want to be tied in for that extra year? on the other hand, four years funding instead of 3 could be a really good thing!
some people say that you should try to go somewhere different for your phd rather than stay at the same institution as it looks better for your cv, but sometimes staying put can be an advantage as you already know people in the dept, know your way around the labs, know where to go for support etc.
money shouldn't be an issue when choosing a phd but unfortunately as the money is so poor it does make it an issue for most people, so perhaps the slightly more generous stipend may help to sway you towards oxford? every extra penny helps when you are surviving on a low income!
there are lots of things to consider but i really feel that you should follow your heart for which project/lab/supervisor suits you best, as these are ultimately the most important things to help keep you sane for the next 3-4 years!
good luck :-)

I'd go for the supervisor. Your project might not work out and have to change. The people in your lab will change during the course of your PhD - you can't predict slight changes in lab culture. The situation regarding opportunities to teach, access to seminars etc. may change or turn out to be better or worse than you expect. But you may well have to interact with your supervisor every day. You're going to be in some way dependent on them for a really long time (how long do you think you'll need them for references, for example?) and they're not going to change.

Which do you feel more comfortable with? Do you think they'll both be equally good at supporting you with writing reports, your thesis, posters and presentations? Do you think they'll both take the time to look out for you - or be "on your side" - in terms of helping you get the most from your PhD and take advantage of the opportunities available? Do you think they'll both motivate and inspire you when you're having a tough time with your project? Is the person you think will be your supervisor the senior person you will interact with on a day to day basis?

Try and choose a supervisor you like: there will be times when they will frustrate and annoy you and it helps if you believe that they are basically a nice person. PhDs are tough enough anyway - you wouldn't want to be in a situation where you dread every meeting or email from your supervisor!

On the other hand if you have strong friendships/ a significant other in Oxford that will help keep you sane... that can add a lot of quality of life too.

Good advice here too: http://www.biology.duke.edu/johnsenlab/advice.html