The polar bear with the black nose is actually the newer version, but now the old version is apparently available again as a DS add on. So I wouldn't call either polar bear rare at all.
I'm sure Tim could fill in on some specific color variations that are very rare. But as to entire species or older molds of species that are rare, there are a few. The woodpecker
http://www.animobil.info/text/3e258fc-1904.html, as we discussed a few days ago, is relatively rare, as compared to other kinds of birds. It is in several sets currently in production, though.
The wildebeest
http://www.animobil.info/text/3e258fc-1187.html is somewhat rare also, being discontinued for many years now. It is seen on ebay regularly, so it is certainly not among the rarest playmobil
items, but it is one of the rarer animals.
Falcons
http://www.animobil.info/text/3e258fc-3112.html seem to have become harder to find lately also. A lot of them came in medieval sets, but I actually don't have one!
And then of course there is the mountain goat:
http://www.animobil.info/text/3e258fc-1064.html which I think must be the rarest animal as far as the rarest mold.
But we must mention certain color variations.... the red nessie, as Arnaud said, and the white mouse, which I have three of thanks to Gis

. I'm sure Tim could fill in a lot more!