The Rosauers on Sprague and University has one of the best beer selections in a grocery store that I have been too. Lot's of single bottles from some good microbreweries, lots of bombers, and a good selection of regular sixers too.
If I'm looking for something special though, I usually run out to Enoteca in Post Falls. They have an incredible wine and beer selection, and both Russell and his wife Sarah are very knowledgeable about both wine and beer. The beer you get there is uaually a little more expensive than what you will find at Bottles, or the rocket bakery on the south hill, but the service and knowledge is well worth the drive and few extra bucks. They also hold beer and wine tastings regularly which are a ton of fun and pretty affordable.