One of the most popular (and most commonly recommended) file integrity monitors is the free, open-source Tripwire, which can be compiled to work on most platforms, including Mac OS X. It's a command-line-only program and somewhat odd to set up, but once you have it configured, you can run it quickly as often as you like to check for and report on file changes since the last run.
Because Tripwire wasn't designed expressly for Mac OS X, it doesn't notice most metadata changes (including changes to file permissions). However, it can effectively report on any content changes, additions, or deletions to any of the files on your disk.
To learn more about what you can do with Tripwire after you've installed it, type man tripwire in Terminal.
To install Tripwire, follow these steps:
Download the Tripwire source code from http://sourceforge.net/projects/tripwire/files. On that page, look for a file with a name similar to tripwire-220.127.116.11-src.tar.bz2 (the version number may vary). Put this file in a location where it's convenient to work with it — for the purpose of these instructions, put it in your home folder.
Open Terminal, located in /Applications/Utilities. Because the shell automatically puts you in your home folder, you need not change directories unless you put the downloaded file somewhere else, in which case type cd to go to that location.
To unarchive the Tripwire source, type tar -xvf tripwire-18.104.22.168-src.tar.bz2 (changing the file name to match yours, if ...