so which is the best in terms of benefits for the students (not money)
MRC, BBRSC, Welcome Trust, EPRSC
Some course and departments seem to have multiple funding bodies - eg. bioinformatics courses.

? I don't quite get the question... once you've got your PhD future employers will be more interested in the department/ reputation of supervisor/your publication(s) out of your PhD. quite frankly, go for the project that interest you /or whatever you can get.

There can be some variation in the financial level of studentships from different funding bodies, but it doesn't matter which one of them does it or if you fund it yourself - it's still a PhD - and it's only a PhD if you submit your thesis and pass your viva.