There are plenty of respected manufacturers out there. I think the first thing you want to settle on is what kind of sound you want, what type of header you want, and what style of muffler you like.
I have read that the flowthrough style mufflers (Magnaflow and Bassani) sound better with an X pipe, while the chambered style (Flowmaster) sound better with an H pipe. Opinions also vary on performance of H versus X.
So try to get settled on what headers you want, and whether you want to go H or X pipe. That will narrow down the options a bit.
I'm sure others can comment more on the merits of various brands from their own experience.