Meld is an awesome tool. There are times when you want to check the difference between two or three files and merge only some parts, it does a great job. You can also compare directories and copy only what you want.
Another tool I always have installed is regexxer, which seems to be unmaintained, unfortunately, but still works great on Debian. It is a search and replace tool, but instead of the usual sed, you watch each file and decide which replacements to perform.