Time to toss in a wrench--what about Super Mario RPG?
It's been a while since I played the game, but I do specifically remember two Toads getting married. There was also a Toad who had a son if I remember right (actually, I think there were several Toads with kids). Given the recent revelations, I'm guessing they chose those genders...or did the parents do it for them?
RPG wasn't the first Mario game I played, and I do remember multiple Toads on screen at a time in others (Super Mario 64 comes to mind) so I was always curious to whether they were all related or whatnot. I recall a bunch of Toads hanging together in Sunshine, and I think they were all "male".
Everyone mentions Toadette, but I really think she was just introduced to balance out the number of male and female characters in Double Dash--aside from her you had Peach, Daisy, and (maybe) Birdo.
Come to think of it, every Toad identified as "male" up until Toadette's debut with the huge exception of Super Mario RPG. (Unless there were "females" in Paper Mario; I actually haven't played through that one).
I know the recent articles have said he's not a mushroom, but if we do take fungi into account, they could reproduce via spores. I don't want to get too in-depth biologically here in terms of how fungi reproduce, but if Toads have any hint of fungi in them, it could explain something.