Sailwave handles both handicap and one-design racing. There is an active support group for this program on Yahoo, which the author, Colin Jenkins, monitors for bug reports and suggestions for new features.
RaceSail from MX Yachts is another Windows-based scoring program, also under active development. This program handles one-design, PHRF (TOT and TOD) and Portsmouth handicap races.
SailRace v. 9.0 (209,354 bytes, May 25/97) is a scoring program for sailing regattas, written by Gerald Bennett (gtbenne@nervm.nerdc.ufl.edu). It handles PHRF and Portsmouth handicaps, and one-design scoring.
Regatta is a Windows based program that apparently handles many different handicapping schemes, as well as one-design scoring, and will produce results in html format for posting on the web.
Race Log is an MS-DOS based one-design scoring program.