I'm making a script that will alert me when an invite request happens, and I'm having trouble figuring out a good queue system.

I tried using Token identifiers to add the channel and nick that invited me, but there's no character I can use to seperate the 2 values that wont conflict with the channel name. How can I add the channel and nick for invite requests to a queue?

A , nor a space will EVER conflict with a channel name as RFC1459 (and the lame IRCnet RFC2811) guarantee that a channel name must never contain either of these characters.

So it is possible to use a comma to seperate both the nick and channel without problems?

Yes, neither a nickname nor a channel name can EVER contain a comma.