Ignoring more advanced things like mixing, extra channels for flaps and retracts, etc, here's the things I use on my computer radio:
1) Electronic trims (no more knocking the trim lever while carrying the tx to the field)
2) Multiple model memory (one transmitter, many planes)
3) Throttle cutoff (flip a lever and the engine shuts off, but doesn't mess up the idle trim)
4) Dual rates (let's me set gentle and agressive throws)
5) Exponential (allows me to desensitize the throws in the middle, resulting in smoother flight, especially when using higher throws)
6) Digital voltage indicator instead of silly little LEDs common in 4 channel tx
7) End point adjustment (simplifies initial setup, but should not be a crutch for avoiding mechanical adjustment of the linkages)

Planes can be flown without the above features, but they definitely make things nicer.