If you had asked me this question two years ago, I woud have said Palm OS, without hesitation. Back then, "Windows CE" devices were bulky, crash prone, expensive, and had too little medical software.
Fast forward to today, and now the Pocket PCs are comparable in size to most Palm OS devices. The price difference has also become less significant. And medical software is readily available (though still not as ubiquitous as Palm, but not far behind).
Most importantly, though, technology has advanced in the handheld market such that the PDA is no longer really a companion to your PC, it is in fact powerful enough to be considered a "pocket computer". And as a tech-saavy friend of mine put succinctly, "A real computer needs a real operating system."
If my school hadn't provided us with Clies, I'd probably be using a Pocket PC right now.