I'd vote for in-game comms. Simple, straightforward, requires no third party programs, and even better, any random players that join our squads don't have to alt-tab out and access our TS channel. Granted, the quality isn't perfect, but it's worked well enough so far.
Of course, if something happens to PlanetSide 2's in-game voice system (I seem to remember it going haywire for a bit a few months back?), then we might want to have an alternative. But until that happens, we'll probably be fine with the standard set-up.