I recommend Diffuse for that, and also for three-way merging: http://diffuse.sourceforge.net/
I do join in recommending Meld for your everyday diff/merge, though. :)
Even though it's commercial I gladly payed for it. It's really fast, does a great job on aligning automatically, easily lets me isolate blocks or do manual align, has rules for comparing files, and I could go on.
note: I use Emacs for many other things so that specific point is not a pro or con for me.
http://www.scootersoftware.com/vbulletin/showthread.php?p=24...
It is a newer commercial product with several rough edges, but now there's a "community edition" to try out (it's possible to use just the diff/merge tool without obtaining a license key to setup the server portion):
http://codicesoftware.blogspot.com/2010/11/building-plastic-...
Unfortunately (for automation's sake), there doesn't seem to be any obvious way to specify a single default output file. So you need to manually save whichever file you merged in to, and then refuse at the prompt to save the rest.
Now, if there were an OSX-native app that does 3-panel merges, I'd gladly switch off of Meld.
http://codicesoftware.blogspot.com/2010/07/xmerge-to-merge-r...
Unfortunately, it is not inexpensive.
Glad to see they're working on implementing that feature, though.
edit: Just curious.