Guiffy Software - Shareware text file compare/smart-merge tool with a 1.2 Java/Swing GUI. For all Java-enabled platforms.
KDiff3 - Compares and merges 2 or 3 files or directories. The file diff shows changes within each line. For Unix and for Windows. Source available under GPL.
One-on-One - Utility to compare one folder or volume with another supports both MAC and PCs.
SoftInterface - WordDocDiff compares two MSWord/Text files side by side. Complements FindInFilesX and CompareFilesX.
Unison - File synchronization tool that allows two replicas of a collection of files. Directories to be stored on different hosts (or different disks on the same host)
Vermont Software - Directory Compare is a Windows shareware utility that compares the files in two directories based on file name
Visual Comparer - Fast compare and merge utility for text files. Strict lexical and syntax highlight. The full-function text editor adapted under ideology of line comparing of files.