Is there a way to do Co-Op (storyline) in WC3? I know you can do skirmishing and such, but I didn't know you could do the storyline too.
No. But there are RPG-type custom maps out there. However, they are mostly designed for several players, so the 2 of you might find them harder.
NWN2 allows coop and like previously said, nearly all games require multiple copies per machine. There are some older games that only require a disc to load the game, then you can swap them. Diablo2 has some .mpq files (I think thats the extension) that if you copy them to the Diablo2 directory, it will not utilize the cd. This is how my brothers, father and I use to play it and the Serious Sam games back in the day, which is another great series. Fighting hordes of enemies over and over.
NWN1 has TONS of expansions that will keep you busy for a long time. Look for the NWN Diamond or Platinum editions.
NWN2 is a system hog and is more linear than the original, but still a solid story. Make sure you both have high end machines.
Baldurs Gate/Icewind Dale series. Another set to keep you busy forever. Came before NWN games and has solid storylines and tons of quests to do.
Gears of War. Recently released...high system requirements. Some bugs I hear.
Rainbow 6 Vegas. Don't spend a lot of money on it as the Coop is the only decent part about it. However, the game is buggy...a system hog and the coop isn't that fun to play through multiple times with the same people. There are older R6 games better received than Vegas...all with coop modes.
Splinter Cell CHAOS Theory. The coop mode in this is REALLY FUN and the missions are really long and will have you autosaving/loading over and over as teamwork is required! However, there is only a handful of missions. The game is cheap and has low system requirements, but your faster computers will enjoy great visuals as well.
DOOM3. There's a coop mod for it called Last Man Standing out there. I never played it more than a few minutes....just like DOOM3 itself.
Halflife 1. Svencoop is the most popular coop mod ever. Brings a lot out of the original game. Although I don't think you actually do the campaign together. But they have tons of custom made maps.