Yes we have. We were using cheap kendas, and have a dedicated trainer wheel. Kendas suck actually, they can be uneven, but they are cheap. We are currently using a worn set of contis off my bike. They seem much more durable and noticeably smoother on the trainer.
Funny, when we first got the trainer, my wife shredded a brand new tyre in one session. She didn't notice the pile of rubber until she finished - owch.