Generally, the mosquito problems move up from the lower to the higher elevations over the course of the summer as temperatures allow them to hatch higher and higher, while their life span runs out first down low. By September, pretty much all of the lower elevations are bug free. There are regional variations, but nothing to worry about other than sun, thin air, less water than in spring, and cold nights with shorter days in between, It's about as nice as it gets up there from a nuisance point of view. Too bad half the vegetation is already dead. A general "brown look" is what takes over and all the nice contrast from the snow in spring and early summer has long melted away.
When there are mosquitoes, I use 100% Deet from REI (Jungle Juice) in a bottle, rub on skin and clothes. Works good enough that I don't mind hiking in late spring/early summer. In fall, I don't pack any repellant. I do have some bear spray on the shelf - maybe that's useful if you're the last hiker out in late fall when bears are looking at that lone hiker as the very last chance to properly to fatten up
