When it comes to G1s, I think that the most HTF ones are some of the Nirvanas: out of them I believe Takara one's are possibly the rarest, seeing as the line didn't sell well in Japan back in the day, and knowning how Japan deals with stuff that isn't popular (see the Takara-related threads in the Nirvana section), there aren't that many of them, and chances of finding one (both the big ones and the babies) are very slim. That is, if there are ANY of them left AT ALL.
When it comes to non-Nirvana ponies amongst the HTF ones would be all the ones already mentioned by couple of people here. Mimic and her wave of TE ponies are often brought up, because, from what I understand, the number of these particular TE ponies was smaller from the other ponies. But really, it's hard to tell, since people had different opinions on this.
Also, some of the mail order ponies are hard to find: particularly Rapunzel an Mommy and Baby Pony.
Oh, and let's not forget about One of a Kind ponies, but I think there already is a separate thread for those, so if anyone's interested, just go and check out the Nirvana sub-forum.