I'm usually naked too. Firstly it feels good and more sexy to be naked and secondly it avoids getting cum on clothes.
On the few occasions I am not naked I've usually just pulled it out from the fly or just opened up my trousers a bit and therefore I might be standing.
This last winter though, there were a couple of nights it seemed a bit cold naked so I wore a onesy (sp?) to sleep in. This has a zip all the way down the front from neck to crotch which works out well for j/o. Instead of pulling it up or off ,like a t-shirt to get it out of the way of the cum, I was able to part it sideways to leave my chest/belly clear.