If flying business class, Qatar is the better option, by far (QSuites, dine-on-demand, no 2-2-2 seating, better food, etc). If economy, the differences are minimal. If taking airports into consideration (for the layover), Qatar is the better one imo, especially if you can access the Al Mourjan lounge.
The only circumstances I'd ever consider Emirates again would be if I were able to get a good deal on a first class seat. Everything else, I'd take Qatar.