We were one of those companies. I remember that you had to alter the order of users added to a group in order to have multiple groups (the equivalent of "channels") with the same member list. We'd use that trick to essentially have per-project channels. It wasn't necessarily super graceful, but it mostly worked.

When we made the jump to Slack in early 2014, we migrated as much of our Skype history as we could, which was _a project_, but again, mostly worked.