Previously, I've written about the diff tool meld, a very nice diff tool.
However, meld requires a graphical environment and this isn't always available. Vim however, is pretty much always available and has a diff tool built-in.
Just start vim as follows:
$ vimdiff file1 file2
Screenshot:
Visually it's pretty self-explanatory. Red parts are not in the other file, blue ones are empty parts where the other file has a red part. What you probably want to know, is how to quickly shift differences between the files.
| dp | The difference is pushed to other file. This is valid when the cursor is on a red part. |
| do | difference is obtained from another file. Use in a blue part. |
There are many options, check out the vim documentation on diff mode.