From what I've read about lithium ion batteries, it's best to keep the battery between 40 and 80 percent. They don't like to be empty or full. But if you don't plan to keep your phone for more than a few years, than do what you want.
I think what the OP is asking is, in the long term, when he's at his desk, is it better to have the phone permanently connected to a charger, or simply let it run off it's battery, once it's fully charged?
I can tell you that leaving my old MacBook Pro plugged in all the time using it as a desktop effectively killed the battery; it could only hold a charge for 5 minutes.
On my new MacBook Pro I broke that bad habit by unplugging it once it's topped off.
If you keep your iPhone docked at your computer all day, I recommend to just unplug the USB end from your computer once it's fully charged that way it won't wreak havoc on the battery life. This way the iPhone is still docked and not charging