I use Notepad++ all the time for quick editing of SQL, Python, XML, and all sorts of other types of files, and when I opened it today, it told me there was an update available, so I updated to 5.3.1 .
Then this afternoon when I went to compare two SQL files using the Compare plugin, I couldn't find it, and spent a good 5 minutes combing through the menus before I realized it was really gone. Arggh!
I use the Compare tool all the time, so I immediately downgraded to version 5.2, where it still works. So just a note of caution if you use Compare in Notepad++, 5.3.1 appears to break it - hopefully they'll get that straightened out soon.