[Suicide Junkie]

Good question.
I can't recall any savegame-busters off the top of my head...

You will have to update your settings.txt, and the AIs will all be upgraded.
Your mod will be changed, so make sure everybody updates at the same time as the PBW host game.
I'd also expect a "gold rush" on drones, ship capture tech, and rapid installation of self-destruct devices.

One of the big factors if deciding to upgrade is the fact that everybody in the game must have SE4 Gold, which can be difficult when there's 20 of you.