"Mistah Joker, he dead."
I think my favorite Mr.Freeze story is the Jim Gordon tie in to the Battle for the Cowl.
The best Riddler story is Batman Confidential #26-28/"A New Dawn", by Nunzio DeFilippis, Christina Weir, drawn by the legend himself, Jose Luis Garcia Lopez.
The New 52 Mr. Freeze story was absolutely great. I know someone will probably argue that point but I've all but given up on what the constantly negative comic 'fans' on these boards think at this point.
Gotta keep my PMA (even on CBR)
Chris Gage from Avengers Academy did a pretty good one in Legends Of The Dark Knight's last year or so (issues #201-203).
"This is COMICS. Aren't you rebels and artists and naysayers? Or are you pervs drunk on your taste of 'fame'?"
Probably Dini's GN if you're talking a proper Freeze story, but IMO the best all around story with Freeze in it is the opening arc of Gotham Central. Chilling. A small but key role
I quite like the one where he faced AzBats & Montoya in the morgue. Kind of creepy, but I enjoyed the take. New Knightfall vol 2 is the trade.
As for the Riddler, I really liked the Batman / Judge Dredd crossover that he appeared in. I can't remember the name of it currently, but Riddler was pretty wicked here in his short role.