Properly caramelized onions freeze and thaw very well, since they are already pretty broken down and much of the moisture is gone.

Since the big factor is the 40-60 minutes on the stove, I make a large batch in several pans. The onions can be cooled a bit and then individual portions in an old ice cube tray and frozen.

Then I can just pop out an onion cube and microwave it until softened, anytime I'd like to add caramelized onions to something.