Madison, Firehole, Gibbon - If you are one of those eager to target lakers on their way out of Hebgen, now is the time to brush the dust off that two-hander and get out there. On my last trip to the Madison (before Hebgen) I was seeing quite a few White Millers flying around as well as some tricos so I wouldn't pack that dry fly rod into storage just yet. Although the lake run hasn't really started in earnest just yet, they are starting to show up slowly and there are still some very nice residents sitting in there to tide you over.
Gallatin - As of 9/11; Terrestrials are still the way to go on the Gallatin. A smaller hopper or ant would do the trick, especially on the sunny afternoons. When those fish aren't looking up, a flashy nymph like a rainbow warrior has been doing well!
Yellowstone River - The fishing on the Stone has picked up slightly, with risers being found above the falls especially when clouds and baetis are present. Subsurface approaches like swinging soft hackles and nymphs are still doing well.
Northeast Corner - As of 9/18; With this rain, the Lamar is officially blown once again. Slough and Soda Butte should be at the very least clouded up a fair bit, so I would stick to the western side of the park if you want to fish within Yellowstone. If you find yourself in the area, a small leech (or very large hopper) should be enough to entice a cutty or two.