Like Anonymous says. Linear keeps charge current constant. Pulse turns charging on and off constantly and the charge current you've chosen will be the average current.
Pulse should give you slightly higher voltage, depending on cells. You're charging at higher amperage but giving the cells time to rest between pulses so they don't heat up as much. The first NiMH cells were very sensitive to charging current.
It is flex charging you don't want on your NiMHs, flex charging reverses the charging current momentarily to condition the cells. (I've heard that GP cells like flex charging and all the stuff we used to our NiCds but couldn't do to Sanyo and Panasonic NiMH because of their fragile construction)
Cole, cells lose capacity over time, they dry out and change their characteristics when the plates get "anodized" and crystals form in the insulation. You could try to slowly discharge the cells to zero and then charge them at 1C to 2C (C=Capacity. 3000 mAHr cells = 3amp charge current = 1C) with pulse charge and flexing until they're very hot, it will probably increase their capacity somewhat. But it could kill them permanently