This is a pretty minor issue compared to most of the things you deal with, but I'm a nice guy (we would make an odd pair, you in your patent stilletos, I taking in water through my battered Air Walks, you snarking while I quietly sip from my bucket of scotch) and I want to make things as easy as possible for my potential agent and Best Friend In The Industry. So: I know copy editors prefer Courier, and quite understandably so, but the best font for markup is not necessarily the friendliest for curling up with a bucket of gin and reading out loud to a poodle, and the copy editor is still in the distant future. I'm curious, therefore, if you personally prefer something more poodle-friendly like Times, and to have italics be italicized. I understand yours is but a single opinion among many, but I am curious. It is a matter of seconds for me to switch; I just want to make life easier others down the pike
There is no way to know or keep track of what font an agent likes. And since I'm an agent, not a copy editor I'd be hard pressed to look at something and tell you what font it is. Yes, I click Select Bodini Bold on my trusty computer when I need to screech in a letter, but I wouldn't know Bodini Bold if I fell over it on a leprechaun infested Fifth Avenue this very morning.
Just make it something your grandma can read and we'll be happy.