In CafeTran this is very well possible: open one TM in TMX edit mode as a translation project and the other one as a normal TM.
Then run Project > Statistics to get an analysis or QA > Translation conformity check to list the project target segments that don't match the TM target segments.
Edit: It seems that it's not yet possible to use this QA for TMX projects (nor is it possible to save TMX project as text only). It would be useful if these would be added in future.
Work-around: Save the source TM in CafeTran as HTML, open the HTML in Word, copy the table to Excel. Create an Excel translation project. Then you can use QA Trans conformity too.
In the meantime, Meta's posting has been approved. The text:
You can compare two TMs directly, or you can convert them to TXT files. I'd go for the latter so you won't see all the mark-up stuff. Your CAT tool can probably take care of the conversion, or you can use Heartsome's TMXEditor (free). You should then use a file comparator, I use (a.o.) <a rel="nofollow" href="http://kdiff3.sourceforge.net">KDIFF3</a> (free).
If your CAT tool can edit TMX files (CafeTran can), you can probably use one TM to "edit", and the other as a TM. Haven't tried that one.
And the steps in a video.