I really detest onion on my burgers, but like most people on this thread have little to no faith in a custom order being put through correctly - once I asked for no onion on a McD's Quarter Pounder and bizarrely got extra lettuce instead, which it doesn't actually come with in the first place!
However, I have found that asking for a burger "plain" with nothing on it seems to work - they'll actually get that order right 99% of the time. So I do that and then ask for a pot of ketchup/mustard/BBQ sauce/whatever condiment I'm in the mood for, and put that on myself.
Oh, but when I am in the States, I always add cheese to a Wendy's Spicy Chicken. Just because I can.