Finding an area that isn't "expensive" can be quite a tall order even if they are in an "up and coming area". Generally speaking your are probably looking at something on the outskirts of zone 2 or zone three these days, with South of the river tending to be less developed than North.
In terms of commute, anything under an hour is general considered good, but it really depends on where you are trying to get to and from (and you can get quick trains from outside of London that get you into the city in under an hour).
With all of that being said, here's a few places worth considering:
If you are looking South - Elephant and Castle, Bermondsey, Peckham, Streatham, Lewisham, Tooting, Crystal Palace
East - Mile End, Bow, Stratford, Popular, Dalston, Stoke Newington, Hackney (although it's pretty far along)
North - Tottenham, Seven Sisters, Mannor House, Kings Cross (although it's pretty far along)
West - Battersea, Southfields, Roehampton
(Sorry, I'm less useful West).