Pembroke you get accommodation on site for 3 years (at least my brother did). Clare you live across Queen Street in the first year, in the Colony in the second year and in college itself in the third year, but the accommodation is still very nice.
Pembroke is very open, has large garden areas and is beautiful. Clare is slightly more closed, but has stone buildings and an area of the backs, making it possible more beautiful - a matter of taste.
Clare is usually harder to get into, though Cambridge topped the Tomkins table a couple of years ago. It's a bit of an anomoly though, in that it's more usually around 3-5th.
It's all about personal taste. Clare is known as *the* friendly college, but everyone I know at Pembroke are absolutely lovely people, so I don't think there's much difference on that score. They're both beautiful, though different; both prestigious and old; both have good accommodation, though I'd give the nod to Pembroke - in short, it's all down to personal taste, though I can't see you going at all wrong with either.