I've found two options in English: the San Juan Star, a storied paper whose brand still persists, and Caribbean Business. I prefer the latter, as the copies of the former I've seen were badly proofed.
The Spanish papers serve me mostly for language practice, so I don't buy the main one, El Nuevo DÃa, except on Sundays. It probably has the best coverage and excellent series. I mostly subsist on the three free papers handed out at traffic intersections. Of these, I feel the most solid is El Vocero, which I think is a member of a group of local (region of Island) papers. Hence, these are excellent for finding local businesses and classifieds.
Be aware that, in all cases, the electronic versions on the Web don't carry all the stories that the paper versions do.
