I did online cooperative works, but also in-house cooperative works.
For in-house, it was fairly easy because we all had laptops (or we went to my office, for those of us who didn't have laptops) and worked together (each taking on a particular project) and kept a list of things to do on our dry-erase board. We also did presentations with each other on my projector, directly from our computers. This way we all knew what the others were working on and could comment and suggest things.
Unfortunately, in the end, we all grew up and stopped working on projects. We were terrible at deciding a single project to work on though, so whilst we were really organised in each project, we only finished a few games. And those games were pretty much only the first ones we attempted, which obviously the first ten games we actually completed... sucked... XD
The others would have done much better, as we had learned and gained experience over a couple years of working together, but we all grew up and went our own ways.
In relation to the online aspect, I didn't use Skype, I used YIM (which I no longer use). My friends in Europe were the only people I worked with on projects at that time, and that was before an incident which disconnected our lead developer, so we all abandoned the project.
It worked well though, for the time that we did it. We sent files back and forth through YIM, and we all talked together in a group chat.
I had at one time built us a forum and a site, but we never used it because we didn't care to get input from others, lol.
I actually used RRR to get many of the resources we used; because the online group had ZERO ability to do anything except for make music and create ideas and story.
So that's that about that. XD
Now, I'm just content to see others work on their projects, despite missing the "good old days" with my in-house team. ^^
It's always fun to have a bunch of teenagers working together on a game, but they grow up and move away pretty fast, lol.