There was a recent contest/challenge to make a wargame out of a limited set of miniatures, and it seems to me that the Conquistadors would have been a great set to do this with - split of box of them up with a friend or family member, and each of you can assemble and paint them in a different faction, and run a few simple skirmishes between, say, the Spanish and Portuguese, any of the Italian states, probably the French, maybe the Swiss... the different armies, I imagine, would have used very similar equipment and armor, distinguished largely only by their banners.
But you need not stop at historical subjects: I can't help noticing that most of Wargames Atlantic's fantasy armies wouldn't look far out of place in the Renaissance, other than the fact that they aren't human: the Halflings, Lizard-Men, Goblins, Ogres would, I think, look fine on a tabletop along side Conquistadors given a more or less fantasy spin. Those conquistadors, if you ask me, are just betting to fight a war against a goblin horde, some ogre Landsknechts, or the lizard men, with a little backup from some valiant Halfling militia!
I don't play Warhammer or 40K, but it wouldn't surprise me to find that there are at least a couple Warhammer factions that the Conquistadors would stand in for, given what I've seen of Warhammer sets in the past. The reverse is probably true, too: if you happen to have a few Warhammer kits or a stash of Warhammer bitz to work with, then I'm sure they'll work fine with thee Conquistadors (and/or Aztecs).
Looking a little bit further afield than GW for fantasy stuff to use with the Conquistadors, it seems to me that the Oathmark and Frostgrave stuff might have som potential. The sculpting of hese kits is a little different from the fairly naturalistic/realistic look of the Conquistadors - tending instead toward shorter, more exaggerated figures, proportions, and features - but will probably mostly mix OK with the Conquistadors with a little care. The bits from the Frostgrave Wizards kits in particular might be of interest here, as would the Frostgrave cultists and knights, for adding some distinctive character figures and equipment to your fantasy Conquistador army!
Someone posted some pictures a few days ago of some of the Conquistador bits added to some Wargames Atlantic Dark Age figure bodies - I think it might have been from an Army Builder set - and the results looked fine, from a fantasy standpoint. Don't be afraid to kitbash your Conquistadors with seemingly odd bits from other eras - the Wargames Atlantic Dark Ages, Roman Empire, Age of Chivalry knights, and even the First Empires Persians ought to give you some great fantasy results.
The upcoming peasants set looks like it might also be great for this purpose! The upcoming zombies kits also looks promising - why not pick up some Digital Atlantic priests and monks and a few boxes of zombies, and lauch an inquisition to stamp out the Zombie Apocalypse, Anno 1666?