BeyondCompare

Beyond Compare was the best tool I've found for comparing program source and other files. It also has a directory compare.

• http://www.scootersoftware.com [on Windows or Linux, purchase licenses] $$

Try WinMerge for a free open source tool.

But you might prefer the free ExamDiff or its shareware version ExamDiff Pro

• http://www.prestosoft.com/ [on Windows; sorry, I can not find the free]

Or Araxis Merge $$

• http://www.araxis.com/merge/index.html [on Windows, try Free for 30 Days]

Or MergeRight $$

• http://www.mergeright.net/

Note that the product seems to be no longer under development