Voldemort and Dumbledore. Let's face it: Punisher's beaten a Doom robot. That was sheer tenacity and firepower. We know that Sirius and little mouse boy both could kill multiple people with a single curse. Dumbledore and Voldemort are far beyond that in power. Voldemort's also undead. Between them, they have spell knowledge that would make Raven and the Scarlet Witch blush (hey, if I can be dirty for a second: how about a Raven/Scarlet Witch match... if you know what I mean.)
Doom may have nasty technology and incredible intelligence, but he's going up against another sinister mastermind who held an entire world of magic fairly much hostage. Voldy and Doom alone would be a fun fight, but add Dumbledore and it's over.