I did a little Spelljammer interlude for a couple of adventures in one 3.5 campaign I'm running. After leaving a tattoo parlor where one PC had just gotten a magical tattoo on his chest (long story), the PCs were "beamed up" by a neogi spelljamming vessel, the first of its kind with such a "transporter" device. The PCs had "agony gems" embedded in their foreheads to prevent their escape, and they were basically forced to be slave-pirates for the neogi. They eventually found a way to escape the ship and have their agony gems removed, but discovered in the meantime that their pixie companion had snuck on board in search of them, and they had inadvertently left her behind.
So, after resting up for a day, they teleported back on board a captured tradesman vessel being towed behind the neogi vessel (which itself was otherwise shielded from teleport spells and the like, except for those stemming from its transporter equipment), thinking to fight their way through the neogi and their umber hulk slaves to rescue their pixie friend (and the dowhar and rastipede slave-pirates that had served with them). They found out that in the meantime, a mind flayer spelljamming vessel had tracked the neogi ship down and was in the midst of trying to take it themselves, to get to the prototype transporter device. So, it ended up being the PCs (and their giff cohort, a Space Marine on shore leave who had likewise been abducted from right outside the tattoo parlor) vs. a neogi vessel - and they relished cutting through the ranks of their erstwhile abductors - only to then have to fight their way through the mind flayer vessel, since the illithids had already consumed the brain of the neogi inventor of the transporter device, and thus would have been able to eventually duplicate it in their own spelljamming vessels. They took on many mind flayers, a pair of urophions (mind flayer ropers), a Large half-illithid dire shark (which swam through the phlogiston guarding the mind flayers' nautiloid vessel), quaggoth slaves, and a ulitherid (a Large mind flayer, the Captain of the vessel), plus the Captain's pet carrion crawler.
Eventually, having cleaned both ships out, they flew the neogi spelljammer straight into a sun before teleporting out at the last moment, to ensure the transporter device never got into the wrong hands. Good times were had by all (although my oldest son absolutely chafed having his PC forced into temporary slave-pirate servitude).
My original plan was to include an adventure between those two, in which the neogi send their slave-pirates into the asteroid where they gain their umber hulk slaves, to discover what's been killing them off. (It would have been an ulgurstaasta.) I had planned a way for them to shake off the agony gems while unsupervised deep inside the asteroid, but my players found a way to do so ahead of time, so there was no need for that whole adventure.
Other than that, though, I don't think I've ever used mind flayers with any regularity. I purposely put them into the plot when I decided to do a couple Spelljammer adventures, though, wishing to correct that imbalance in my monster repertoire.
Johnathan
There were many displeased players for the few moments until it was told to those who didn't make the Spellcraft check during the initial Astral Spell ritual that they were astral projections that whole time.
