Ok, good topic.
In my area we have 2 flyshops and a Sportsmans warehouse.
One flyshop feels they are the only place in town and if your not going to drop some major coin they are really not that helpful so therefor I won't mention their name.
Sportsmans Warehouse has the best selection of rods and materials, but the staff is a little lackluster.
The other is Anglers Den, managed by a guy that I have dealt with for years, Wade Jacklin, he's always very helpful, never makes you feel rushed, always willing to spend time with customers whether they are new to the sport or been doing it for years.
As far as other shops, Dorian mentioned Jimmys' in Idaho Falls, very good shop and all that he mentioned is true.
SouthFork outfitters on the banks of the South Fork of the Snake River(near Swan Valley) has a very nice shop, knowledgable staff and first rate guides, the down side for them is that their lodging is tailored for high end clients and the restaurant is ok but a little too ritzy for me, they do have a bar that serves a better albeit smaller menu but the beer is always cold.
In this area if you want a killer burger go to the 'Fox's cornered bar' in Swan Valley.
If your on the Henry's Fork in Last Chance Idaho, stop in to the Trouthunter, they have very good guides, hand selected fly tying materials from the 'House of Harrop', not to mention 'HOH' flies and top notch equipment.
The restaurant is great, if your there in the Summer they often times will have live bands playing inhouse, and the rooms are very nice too.
And across the street you have the new home for 'Henry's Fork Anglers'(same spot, new building) which is still run by Mike Lawson. the place is amazing, and has a fancy Coffee shop upstairs, if you go you have to check out Mikes' aquarium
Another place to check out in Last Chance is the 'Grub Stake' general store and gas station run by Brad and Dionne Smith.
Brad is a very accomplished flyfisherman, has a small selection of flies, and a good selection of beer and wine, they also put on one helluva 4th of July fire works show, just bring your own lawn chairs.
And the #1 reason to stop in, Dionne makes the best darn deli sandwich around, have her put the homemade mustard on it too!! thinkin about it makes my mouth water.