I don't like ViNCEd (the shell/console shipped with OS3.9) so I'd recommend KingCON.
Visage is a good image-viewer.
HippoPlayer if you want to listen to modules.
A good port or clone of "ls" always comes in handy.
If you want a do-all system patcher/improver I'd have to say MCP (Master Control Program). I've been using it since 1996 and I couldn't live without it.
