In Merlin fandom, I think basically anything other than Arthur/Merlin could reasonably be considered a rare-pair, but I can't bring myself to call Arthur/Gwen a rare-pair because it's the primary ship that the canon itself pushes. Canon doesn't automatically equal popular, I'd certainly still consider stuff like Merlin/Freya and Gaius/Alice to be rare-pairs, but I think Arthur/Gwen is probably the ship with the second-biggest representation in fanworks after Arthur/Merlin, so between that and the canon, I don't think it counts any more. (It certainly did before series 2 aired, of course.)

Gwen/Morgana is major as far as femslash goes, but femslash itself is such a small corner of the fandom that I can't see any femslash pairing not being a rarepair. (Well, unless it's gender-swapped Arthur/Merlin.)

I feel like Merlin fandom kind of has two levels of rare-pair. There's Arthur/Merlin and Arthur/Gwen as the big ones, then stuff like Merlin/Gwaine, Arthur/Percival, Merlin/Morgana, Arthur/Morgana, Gwen/Morgana, Morgana/Morgause, which have solid followings even if they're not that well-represented overall, and then there's the really obscure stuff like Gwen/Merlin, Uther/Gaius, and pretty much any pairing involving a one-off character - the ones that don't have their own communities or more than a handful of fics focussed on them together.