There are things such as tripwire that can do this on a system-wide basis.

Update: Sorry, add a bit of context for the non-sysadmin types who may never have heard of it.

Tripwire is a system integrity checker. You run it after you've installed a new system to generate a database of what the filesystem should look like (what user/group owns what files, their permissions, checksums). The software then is used to periodically scan for anything that doesn't match up with the baseline. When you (legitimately) update the system (install patches or new versions of software) you re-establish a new baseline and then that'll be used from then on. It's original use was as a local intrusion detection tool (griping if things that might be tampered with by a root-kit are not what they should be), but it'd be useable for the purpose mentioned in the OP as well.