I'd prick them out when about .75 or 1 cm in height, or more accurately, I wouldn't "prick" them out but rather, empty the whole potful onto my potting bench and separate them to individuals, and pot each alone. If you tip out the potful rather than digging each from the pot, you avoid root damage. I have most trouble with Gentiana verna and nowadays tend to pot up small "pinches" of several seedlings rather than singles. At least one or two survive in each pot.
I have a couple of pots with G. acaulis and G. angustifolia seedlings. They should already have been done being now over 1 cm high but there just wasn't time in the autumn before the weather broke. I like to pot seedlings only in spring, summer and early autumn so that new roots can establish before it gets too cold. They'll take careful separation, come the spring.