[Jmacq1]

With all their resources? Doom, easily. In point of fact, he's used devices that negate mutant powers on multiple occasions. Once it reaches a personal confrontation, it becomes Doom vs. a powerless Magneto. Short fight.

Doom is also smarter than Magneto by a pretty wide margin. Not that Magneto isn't a genius, it's just that Doom is explicitly one of the two smartest guys on the planet. Given even a minimum of time to prepare, Magneto is likely to get trounced in anything except maybe a popularity contest.

If it were a drop of the hat "standard equipment" battle...Magneto, almost as easily as Doom vs. Powerless Magneto. There's no evidence that Doom's "mutant power negators" are standard equipment (he doesn't have them built into his suit all the time, in other words). Without that power negator, there are a vast multitude of ways Magneto could effectively defeat Doom despite his armor (or because of it). -Killing- Doom might be much harder though, due to his magical abilities and his "Ovoid Mind Transfer" technique.