I hope I haven't just given myself a third job!
Dear Euclid,
Oh boy, a good question you pose.
A partial answer: they definately would not have used galleys of any sort. Those were strictly military vessels and lacked the displacement to even carry decent supplies for their crew, much less storage or berthing for horses.
As for the best hypothesis for how horses were transported read the following:
Hyland, Ann., The Medieval Warhorse., 1996, Combined Books, Pennsylvania, ISBN 0-938289-84-5. (Chapter 8: the importance of the Horse in the Crusades., p. 140-168) The author gives actual vessel dimensions of vessels used in later Crusades, but indicates that in the early Crusades (c. 1100) vessels couldn't take horses on long sea voyages due to lack of capacity. (cite: p. 144).
The problem with exactly what kind of ship was used is that the all information I've ever read is about northern Europe where they used lapstrake hulls (similar to Viking ships) while the Mediterranean used the caravel type planked hull. Also, this was the time when the modern rudder began to replace steerboards. The north European ships used at the time tended to look like Viking Knorrs (deep hulled merchant vessels), but were starting to have a small sterncastle added to the back. Those vessels were almost uniformly single masted, square sailed ships with one big sail.
I have a series of photographs I took in Winchester Cathedral of the baptismal font of John Lackland (the evil Prince John of Robin Hood legend) showing the first rudder equipped ship ever shown in an English depiction. I'd say you can likely Google the words Baptismal Font of King John (or Prince John) since somebody most have put up images on-line by now.
I just can't tell you exactly what the ships in that part of the world would have been like and give you a citation to follow up on. You might be able to find some images from the recent underwater surveys of wrecks in the Black Sea (google that phrase), and try emailing the Ukrainian or other university groups who did the work to see if they'd be willing to share images. While normally there is not much to look at from a wooden ship after only a few decades underwater, the images I've seen from the black sea have been astounding due to the unique deep water conditions that inhibited wood decay.
If you want me to guess what the ships looked like I'd be willing to hazard the guess, but I know you need more than an educated guess from somebody you don't know. All I can say is that you should be able to run down that information.
Oh yes, what I do know is that the Venetians completely dominated the Adriatic Sea. Any ships sailing those waters did so entirely at the whim of the Serene Republic. Look up Venetian history and you just might find what an early medieval merchant ship from Venice is supposed to look like.
Hope that helps. That one is a tough question.
PS: I hope you do know that they weren't riding horses like modern Draft Shires or Clydesdales then either (wife insisted I post that fact).