There are several options available for two-handed weapons in 4e.
Ignoring build, is there a qualified best option? Analysis in each category would be welcome. What are the best options for Simple Melee, Military Melee and Superior weapons?
The best two handed weapon not taking into consideration build and in terms of damage die and weapon proficiency bonus would probably be the Full Blade from the Adventurer's Vault. With +3 proficiency bonus and 1d12 damage I'm pretty sure it has the highest numbers.
It depends on intention and synergy from feats. Looking at only the weapons themselves, the Execution Axe has a .075 DPR increase over the Mordenkrad. That's not much. Considering common magical items and feats, the Gouge is best from a whole-character point of view.
First, let's look at the superior weapons available to us that are two-handed and interesting:
Statistically speaking, these are all functionally equivalent without looking at magic item or feat synergy.
Generally the only builds that care about big weapons are focused on charging, and at higher levels the choice of weapon is increasingly constrained by the specific build of the character: higher level chargers will have their choice of weapon dictated by their feats, class features, and magical items. This means that it's only at relatively low levels that a weapon's damage and proficiency bonus are significant considerations.
Most classes have feats and class features that guide towards a specific weapon group. Clearly, this is setting aside plot-relevant choices. Beyond that, most characters' damage comes from the static modifiers added on top of the attack instead of the weapon itself.
The Mordenkrad has the absolutely exceptional Avalanche Hammer which just adds an extra 1[W] on top when you charge.
The Gouge has Surprising Charge (feat), Spear Expertise (bonus on damage when charging) and Vanguard weapon, for a total of an extra 1[W]+1+1d8 on a charge.
The Execution Axe has a not particularly useful expertise (there are some edge cases, but they don't matter statistically speaking) and Vanguard weapon.
And the fullblade has... vanguard weapon. Technically, the increase in accuracy can be claimed to be worth the decrease in overall damage due to the fact that you've got extra stuff on your powers that occur, but that is a function of specific optimization, not general "what's the best weapon."