Kuhnhenn's Brewery in Warren is, In my opinion, the best brewer in Michigan. They don't distribute, so they're not as well known as the rest, but their selection beats any other brewery in the state, except maybe Bells or ABC. They also have a ton of wines and meads, a brew store next door, and sometimes even live entertainment.
Check them out online at Kuhnhenn Brewing Co., or you can also check them out at the Michigan Beerfest; they usually come to impress. ^_^
Another plug for Arcadia for great food and beer - and usually something interesting on cask. Their Hop Rocket is superb. North Peak in Traverse city also has great food and draft beer, but their bottled stuff is not so great (different brewery).
Favorite Michigan beer at the moment is Founder's Backwoods Bastard. Best wood aged beer I've ever tasted.
Others -
Celis Grand Cru - Michigan Brewing Company
Too Cream Stout - Dark Horse
Two Hearted Ale - Bell's
Founders Porter, Red's Rye, and KBS
New Holland Night Tripper - an imperial stout no longer in production, but still sometimes found on shelves nicely aged.
Black Forest: Real good robust porter and IPA last trip!
Bells: Two-Hearted and Expedition Stout come to mind
Founders: Centennial and all the Dirty Bastards
Khunnenns: DRIPA, and many others, including their meads
Fort Street: A cask ale tapping each week?!?!
My personal favorites that I've been to so far are Keweenaw Brewing Company in Houghton, Right Brain in Traverse City, North Peak in Traverse City, and Founders in Grand Rapids. I love New Holland, but I haven't had a chance to actually visit yet.