Obviously there are lots of great flyshops around the country and this list is short so get out there and find a few of your own. I can speak for the great service in the shops listed simply because I've been there and seen it firsthand.
My go to shop around the Springfield/Branson area. Brett Rader has not only the best fly shop in the area, but runs a guide service that is second to none. Brett taught me a lot of what I know about fishing tailwaters over the years of frequenting his shop. If you want to catch more fish, period, spend a day or two with this guy. He also has some of the hottest patterns available for fishing in not only his home waters of Taneycomo but anywhere in the country. His G-Bug pattern has caught trout for me everywhere I've fished from Colorado to the Ozarks and more often than not you'll find his baitfish jig pattern as my point fly on a two nymph rig in fast water.
K&K Fly Fishers........Overland Park, Kansas
This is my local shop that I frequent for the weekly or sometimes daily items needed for fly tying or a last minute item for a trip. Everyone in the shop is not only extremely nice but very knowledgeable about a wide range of fishing types and destinations. Great selection of fly tying materials.
Frying Pan Anglers.....Basalt, Colorado
Got some great information from these guys while out in the area last year fishing the Frying Pan. They were very willing to help and the advice was spot on. A huge selection of some of the best looking local patterns we found anywhere in the area. If you're in Basalt fishing the "Fork" or the "Pan" you need to stop in and check with these guys.
Readings Fly Shop.....Lebanon, Missouri
A real fishermans fly shop with a casting pool out front and an eclectic array of items to browse through. This is the kind of shop that you can spend an hour walking around in and still miss something you just might need. A great place to spend a couple hours on a nasty weather day picking up some fly tying supplies and browsing through the fly fishing book section of the store.
Kirk's Flyshop......Estes Park, Colorado
A great little flyshop located in downtown Estes Park. While the wife and I were staying in Rocky Mountain National Park this was my go to shop for info on what lakes and streams were fishing good. The gentleman running the shop was very helpful to a first timer in the park and pointed me in the right direction for some outstanding fishing. They're a fully stocked flyshop with everything you might need to outfit you for some backcountry fishing in the park.
FlyBox Outfitters......Kennesaw, Georgia
I visited this small shop several times while in the area for training this fall. We were looking for information on the local waters, particularly the "Hooch" as they call it, and Willie the shop manager was more than willing to spend the time to fill us in on areas to fish ,local hot patterns, and what we should expect. He gave us the kind of attention that you won't find in any of those big box stores. We took his help and turned it into a great evening of fishing on a river that was totally new to us , and that's what it's all about after all.
Yager's Flyshop......Lawrence , Kansas
I've only been in this shop a couple times and both of these were to pick up a particular item I had in mind. It's a small shop with a good selection of both warmwater and coldwater flyfishing supplies , but the main reason to visit this shop is the helpfulness and friendly attitude of the gentleman running the store. If they don't stock what you want , they'll do their best to get it for you. It's one of those shops where you're made to feel welcome as soon as you walk through the door , kind of like sitting around telling stories with an old fishing buddy. Tackle stores are a dime a dozen while flyshops with friendly people that go out of their way to help you out are getting harder to find. It's places like this that we all need to support before they're a thing of the past.
Mountain River FlyShop....Cotter , Arkansas
A great flyshop located in Cotter Arkansas along the famous White River. Since being moved and remodeled by current owner Steve Dally this once small flyshop has really grown and is now a large full service shop that can set you up with any number of guides , outfit you with the best gear and fill your flyboxes with the hottest patterns for the river. While on the White recently I made two stops in the shop , to pick up a few new streamers upon arrival and then again to stock up on a few tying supplies on my way out of town. I was impressed with their selection of flies and equipment as well as their tying section. The shop is decorated with lots of wonderful flyfishing artwork which is well worth taking some time to walk around and look at. Maybe the most important thing was that the folks running the shop are great people , willing to help out someone new to the river or just trade fishing stories if that's what you're looking to do. Next time you're down in the area make it a point to stop in....you won't be disappointed.