Clare and Trinity Hall both have accommodation that's spread across the town, so you won't be on the main site all the time - if you like it all (likely with Clare's, famously pretty - Trinity Hall's is long way away from the centre I think) that's great but you might wanna check. Don't know about John's/Magdalene.
Jesus pros/cons I considered:
PROS
1. 5 min walk from the centre but tourists don't know it exists.
2. Huge grounds w/grass and pitches and ORCHARD
3. All accommodation within 2 min walk, for all years (2nd 3rd yrs can live in College houses in the surrounding street)
4. Food is supposed to be great
5. Bar is supposed to be pretty good
6. Accommodation is very good from what I've seen
7. Really good sports if that's your thing
8. 2 min from the ADC if Drama's your thing
9. Not stupidly big but not teeny either.
10. Really, REALLY pretty library.
CONS
1. From what I've seen so far they allocate freshers' rooms randomly (- but P6?)
2. Across town from the Sidgwick site - not sure where the Geography faculty is but that's my site xD Still only a 15 min walk though.
3. ???
I ended up applying to J which is why I know more about it than other colleges xD the other two I mentioned I just looked around before I got to the Open Day stage, but it was the accommodation thing that ended up drawing me away from them and towards Jesus.
Hope this was vaguely helpful, sorry for the length!