I was in St. Paul, Minnesota last month and visited three yarn shops: Three Kittens, The Yarnery, and Borealis Yarns.
1) Three Kittens Yarn Shoppe has a lot to offer the serious knitter (oodles of yarn crammed into every available space, large selection of buttons) but they had a temporary? odor problem. I'm not a delicate flower about odors so it had to be pretty bad if it chased me out of the store early. Otherwise I could've easily spent an entire day looking at all the yarn -- and boy do they have plenty of yarn -- and daydreaming. Don't pass up an opportunity to visit this shop if you're in the Twin Cities. (I'm assuming the problem is temporary because nobody else has mentioned it in their online reviews.)
2) The Yarnery is smaller but easy to love, they were having a 20% off everything sale! I left with a few skeins of super-cheap Plymouth Encore DK to make a zip-up-the-back hoodie for my brother's baby. (Photo coming soon, I just need to block it and sew in the zipper.) The shop interior is clean and organized, which isn't what I expected from a yarn shop that's been in business for 30+ years -- you know how cluttered those can be (see Three Kittens). I'm assuming they moved or remodelled in the recent past because really, the shop looks like a new yarn shop located in an old house. My only complaint, and it's not a deal-breaker, is the pattern closet. They have about two-three dozen pattern binders, which is a lot more than the average shop, but they're stored in a tiny closet. This makes it hard for more than one person to browse the patterns at a time. Ideally people would grab the binder they want and look through it at the nearby table to free up closet space but some people are oblivious to other shoppers breathing down their necks.
3) Borealis Yarns was the third and final shop we visited. By then my desire to look at yarn I can't afford had been sated (and I was eager to see my brother) so we breezed in and out and didn't give it a fair shake. They had the cutest Fiber Trends hedgehogs on display, which is the best use of novelty yarn I've seen. I dare you to click on that link to see just how cute. I wouldn't mind going back to Borealis but it'll be the first stop so I'm not yarned out by the time I get there.