Puppet and Chef are pretty agnostic. You can use them to manage only your infrastructure (packages, user accounts, databases) and leave app deployment up to something like capistrano or fabric if you like (although at a certain level of app complexity it makes sense to integrate.)

cfengine has been around longer, but seems to have negative adoption since puppet became well-known. I know a few people who swear by it, though.

FWIW, at my current startup I use Chef to manage a mid-sized collection of servers (app, load balancers, DBs/replicas, task processors) where the app is written mostly in Python, and it took a ton of pain out of scaling up to deal with a very large paying customer two nights ago.

Puppet has better documentation, but learning either is a bit of a trial and error process I think. You might find Blueprint (https://github.com/devstructure/blueprint) useful to bootstrap (the authors are around in the HN community, I think.)