trans flushes usualy run anywhere between $90-$150. Usually. I'd go to a place that'll let you watch them completly flush the system too. You can do a coolant flush yourself, but it would run about the same price range as a tranny flush I would think, mabye less. Avoid jiffylube.
auto tranny flushes should be done (depending on how hard you are on it)
between 35-60K miles
manual flushes (ditto variables) 50-80K
I'd say those are a good set of minnimal intervule flushes.. most people go ahead and do less, just because it's a "relatively" cheap way to keep your transmission alive and well.
ATX's also have oil filters.. which need to be replaced every time you flush as well. A good tranny shop will replace the oil-pan gasket when they do a ATX flush.
