A friend has given me a tray of potted-up chilli & pepper seedlings but unfortunately they're not labelled. As I normally plant my mature chillies in slightly smaller pots than the peppers I wonder if there's any way of identifying them as they grow bigger. They all look identical at the moment.

I think you are unlucky. There might be a tendency for chilli peppers to have slightly smaller leaves if they are the pointy ones but habanero have broader leaves and it would be a while before any difference shows, on balance I think no chance.

It ought to be possible to distinguish them as they develop. But it can be complicated. For instance, some chillies are a different species from the sweet pepper, and one of them is quite hairy (I forget which), but most are selections of the same species (C. annuum) — sweet peppers are chillies without the heat, and with generally larger fruits. What you might see is larger, broader foliage on your sweet peppers, as opposed to most chillies which tend to have smaller and more numerous leaves. But then it depends on the variety, even so. Long Spanish sweet pepper varieties, such as Corno di Toro, can look very like a chilli when growing.
In conclusion, there's a fair probability that the chilli variety you're growing will have smaller leaves than your pepper. That's how you will be able to distinguish them.

yes, I realise it's probably going to be well nigh impossible having grown them both regularly in the past. I think I'll probably have to wait until the fruits start developing and then decide whether what I think are the peppers need potting on into a bigger pot.

The hairy one is Capsicum Pubescens which is easily recognisable from 2 true leaf stage onwards, but is also rather uncommon. It is also possible to distinguish Capsicum Chinense (the numbingly hot fruity ones like Habanero, Scotch bonnet) from other species quite early because of leaf characteristics.

But more likely than not, they are all Capsicum Annuum, and thus quite difficult to tell apart ...