Oli had cat flu when I got him at 13 weeks old (and he was from a cattery!) He had watery, conjunctivitis (sp?) looking eyes and sneezed alot. The day after I got him I thought he was going to die coz he had no energy and just led still. Poor baby!!
We took him to the vets straight away and he was checked over and given a jab (antibiotic I think, coz he was rather down in the dumps!). We asked the vet how long it would take Oli to recover and if he would be ok and the vet said to keep him warm and keep a close eye on him. We wanted Oli to have his kitten vaccinations, but coz of the cat flu we had to wait several weeks for him to recover before he could have them.
As well as having the cat flu, the vet suspected chlamidia (eyes), so we had to put cream in his eyes twice a day for three weeks. He was also allergic to mites so had thick black scabby looking ears. We had to put drops in his ears too!
Now, which the vets believes to have been caused by cat flu, Oli has a blocked tear duct (so looks like he is crying and sometimes has dirty looking fur around his one eye) and something behind the eye is damaged. This causes him to often have very sore, red looking eyes which wink alot. There is no treatment for this.
We, at home have noticed that Oli's sight doesnt appear to be that great. Mind you, he could just be a dopey cat!

For example: Our friend stroked him on the side, but he didnt see her hand and jumped a mile. He also regularly misjudges the wall, when trying to dodge us and usually ends up banging into the wall or door frame.
I think cat flu is common in catteries due to the number of cats coming and going all the time. You may find this link helpful ...
http://www.fabcats.org/catflu1.html