Caramelised onions seem easier to make in large batches, so could I make a big batch then freeze them in say, ice cube trays, for later use? Or would this have a detrimental effect on them?
I would say it depends. I find once you freeze an item the flavor/texture/propeties of the item is changed (for better or for worse) the next time you goto use it.
If your using caramelized onions in a soup, or stew, something where flavors blend together for a longer period of time, then yes go ahead.
however if your using the caramelized onions on top of a steak or something similar. Then my answer would be no.
They will keep reasonably well if you put them in a clean jar and cover in oil.
I've never done this myself, but my guess is that the primary negative effect is that they may become mushy; being as they're mushy already, I'm pretty sure you can go right ahead.
I agree with Tree77. Depends on what you plan on using them for. I've successfully frozen them and used them in risotto, but risotto simmers for quite some time so the onions are almost liquefied by the end anyway. I would say if you plan to try this as a garnish on something like meat, you should get a better then usual vacuum seal on them before freezing and even then it might not work out.