I personally would exclude both of those directories due to the massive amount of (temporary) files they contain. I don't think that would cause any problems.

Hmm, maybe the weird issues are permissions related?

When I load a site onto our dev server from a local MAMP install, many images simply don't show.

If I run a 777 on the files directory, the images start to appear but then it seems like Transmit hangs (or seems to take hours changing all the permissions on the files).

I thought I read something about setting up apache as a user with disk access/rights which bypasses octal permissions.

Does that sound like fantasy or fact?

I doubt that git is your problem here, but if it is deploying your assets with the wrong permissions, you can check by entering the path to where the asset (image file or whatever) should be directly in your browser's address bar.

When you migrate from local development to a testing environment are also synchronizing the database? Because Concrete5 is going to assign your managed files different paths/file IDs, and git can't help you there.

I exclude both of those and never have any problems.

You can exclude git permissions from tracking with

See
http://stackoverflow.com/questions/1580596/how-do-i-make-git-ignore...

You also might want to not track the core and updates as well if you aren't touching any of them. I find this just makes it more confusing.

I also typically ignore the packages directory and track packages separately if at all depending on the package.