Disclaimer: It is entirely possible that someone on this forum has already thought of this idea, and posted it. If this is the case, my most sincere apologies -- it is not my intent to hijack your idea. I have searched the Runebound forums and not seen this idea posted before, so I am offering it to you all now.

Our game group is composed largely of old RPG geezers, and we still spend most of our time on pen & paper rpgs, but we like to vary it up with some board games every now and then. Our favorite is Arkham Horror, but lately we have been giving Runebound some play as well. Though we have nothing against competitive play, our instincts (along with a desire to finish the game in under 6 hours) lead us toward co-op, and so we have been considering some ways to incorporate more co-op play into Runebound, while doing the least possible violence to the existing rules and format.
Voila, then, my Co-op Variant for Runebound...

The essence of this variant can be summarized in one sentence: When two (or more) heroes are in the same board space, one may serve as an ally of the other during a challenge.

In practice, this is how the rule works:
1) Two players decide to take on a challenge together. This will usually be an undefeated challenge that is already on the board, since the players can readily see if they have the skills or equipment required to defeat it. The players decide who will be the ally, and who will take the lead during the challenge.
2) The hero who is to be the ally moves into the space first, but does not trigger the encounter.
3) Then, the hero who will lead the encounter moves into the space, and triggers it. During the subsequent challenge, this hero may use the other hero as an ally, exactly as if he/she were an ally card and not a hero. (That is, the hero who is "guest starring" as an ally can make an attack during one phase of the challenge.) If the hero who is leading the encounter already has two allies, he must turn one face down -- he will not get the use of that ally during this challenge. (This is to preserve the existing restriction on the number of allies allowed.)
4) Likewise, the hero who is serving as an ally does not get the use of his own allies -- he is doing a cameo appearance here, so his own allies get the encounter off. He does, however, get to use his weapons, armor, and other items, as these are his personal property.
5) If either player is KO'd during the challenge, he is removed to the nearest city and the normal rules applied.
6) If the players are successful in defeating the challenge, they may divide the rewards (experience points, gold) as they see fit.
7) Optional Keeper Card Rule: Some challenge cards can be kept once defeated and used later to mess with your competition. If you desire to be nice and play co-op, you may elect instead to sell these cards during a market phase, for one gold per challenge level (that is, green = 1 gold, yellow = 2 gold, and so on).

And that's all there is to it. This mod does not require any major alterations to the basic game rules, any special phase rules, or anything else. If you wish, you can alter the victory conditions of the scenario to reflect co-op play (make them tougher), or you can just let those who want to use it do so, while others continue to play competitively.
Thanks for your attention, and have a great time gaming.
Rags