[lt]

I love Beyond Compare: http://www.scootersoftware.com/

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.

[mkramlich]

I loved it too. Only Windows app I miss since switching to Mac/Linux only.

[dragonquest]

BC version 3 now comes with Linux support in nice little deb, rpm and tarred packages.