The Happy Mondays were the worst of Manchester. They have a few good songs, but the best stuff they released was the Hallelujah EP, and it was all remixes. Now the Stone Roses on the other hand...oh man.
From the Manchester baggy era, I think my faves are the Stone Roses, Inspiral Carpets, Charlatans UK (OK, they're from Norwich), and Northside. Inspiral Carpets put on the most psychedelic show I've ever seen...strobes, slide projections, just the most insane visuals that you can't even imagine. I know, sounds very Pink Floyd, but they were far more 60's garage than anything else. Carter the Unstoppable Sex Machine put on one hell of a light show too. Those were some fun concerts.