Aridia is a rom editor for Phantasy Star III. It has a mostly-friendly interface that makes editing incredibly easy. No messing with hex editors, decoding values, or any of that. If you can click and type then you can hack away to your heart's contentment.
Eisfrei is a ROM editor for Herzog Zwei that allows editing of text, unit attributes, order attributes, and tile-based graphics.
Hapsby is a save state/save game editor for Java compatible platforms. It currently supports over 30 games, adding support for new games is relatively uncomplicated.
Power-Ups are a collection of single-game save state editors and cheating utilities. They're each designed to edit a single aspect from a specific game. They're things that are too complicated to fit into Hapsby but not something I want to devote a huge Aridia-like effort to.
Falcom offers a number of nifty freeware programs on their web site.. unfortunately they're all in Japanese. Despite not being able to read Japanese I decided to translate some of them to English.