There's a few contexts that sentence is used, sadly they all suck ;-)

It should ONLY be used to congratulate/encourage someone, for the example above when a kid does well at footy, best on field or whatever.
It should be used to highlight an achievment!

I know people use it to highlight your finacial status, they walk into a lovely home and the first thing said is "Gee, you've done well", or commenting on a new car etc....i HATE that...."i didn't do well", "i worked damn hard" to achieve that car, house whatever...

If anyone said that to me simply for filling petrol (hardly an achievment)? i'd be quite likely to rip his headoff, maybe then i've done well ;-)
 
MM.