D-Sub, 9, 15 or even 25 pin are good for when you need a high pin density, but as you say are an all or nothing solution.

Jack plugs have their place for 2 to 4 poles but I'm not a fan, after a few good twists and pulls the connectors can bend leading to intermittent contact.

Phonos can be nice, especially the locking versions

My favourite low pin count connectors have to be XLRs. Good for something like 3 Amps at a push they usually feature positive locking and are designed to take abuse. Not very space efficient but you pays yer money and takes yer choice
http://www.rapidonline.com/Cables-Co...udio-Video/XLR

Don't forget the plug in terminal block option, very flexible
http://www.rapidonline.com/Cables-Co...ocks/Pluggable