Seriously, over the years, it seems like he's been named the father of like 100 of them. Anyone know who they all are, dating as far back as...whenever?

the answer to your question can be said, but seriously, it would take some time and research to find all the names.
but here is the names i can say of the bat:

Anthony
Alexandra
Elvis (EJ. by artificial insimination)

can't recall the name..was it Daphne? i think so. Brenda Benet was the actress that played the role back in the mid '80's.

Benji (adopted wasn't he?)
Kristen Blake (step daughter)
Peter Blake (step son)

ok, that's 7 in total including adoption and marriage. i know there are more but i wasn't watching the show between the spring of '82 thru July 9, 1993. so i missed alot. i have read the history, but i can't remember everything.
hope that's a good start for your quest...

Stefano is also the father of Renee DuMonde and Megan Hathaway. Daphne DiMera is not his daughter, Stefano and Daphne were married.
Also Benjy Hawk is Stefano's biological son, but he was killed, I think last year. Renee and Megan are also deceased.

that's right, it was renee who i was thinking and not daphne...thanks for the clarification.
see, i missed alot. and read alot of history..just can't remember it all.