I can't think of any standouts myself- in fact these stories tended to be disappointments, much of the time, for me: I remember one with the Egyptian god Set as the villain, for instance, that I thought should have had much more potential than was realised on the page - though admittedly this was during a long, humdrum period for the series in general (this particular story was around the #240s or 250s, I think).

Pluto was a recurring villain dating back to the Kirby/Lee days, but again, these weren't among my favourites, though I found pretty much everything from their run at least entertaining and fun. Could be I'm forgetting some good ones that someone else will remind us of.

One that was interesting, though a just a one-off, was the issue right after the big Celestials epic finished, around #300 or #301, where Thor went around to all the different pantheons asking for a fraction of their divine energy so he could reconstitute Odin and the Asgardians, or something like that.

I think perhaps one reason I dn't recall many stories of this kind that I liked is because the basic premise doesn't agree with me: there tends to be a sort of "our gods are better than your gods" feeling at the bottom of it, even if not always acknowledged explicitly. Not only is this a dangerously divisive way of thinking, I believe it's at odds with the pagan or pre-Judaeo-Christian outlook I like to think is part of the Thor series at its most interesting.

Not that this attitude never made itself felt in pagan culture at all, but it was less systematic, less all-pervasive, less ingrained into the very basis of their world-view. To take a famous example, when the Trojans and the Achaeans go to war in the Iliad, we don't have a Trojan/Asian pantheon fighting an Achaean/Greek pantheon of national gods: there's just one set, one universal pantheon of gods acknowledged by both sides and the division of pro-Trojan vs pro-Achaean gods is one that occurs within that single pantheon. I think that we moderns tend to take the Judaeo-Christian idea of "our" gods vs theirs so much for granted that we forget to keep this important difference in mind when we read things like the Iliad.