From Ronzo's blog: During the early days of Monkey Island I didn't have a name for Guybrush. We just called him the 'guy'. When Steve Purcell was doing concepts for 'the guy' he was doing them in dpaint. In dpaint you could select a section of the screen called a 'brush' and save it out. It was these files I got from Steve. I saw the file names so many times that the name 'guybrush' stuck.
(Incidentally, Tim Schafer wanted to name the character Hank Plank.
Source: Tim's tweets.)
Threepwood was decided in a company contest. The name comes from the book The Brinkmanship of Galahad Threepwood
(US title). Threepwood
is also rumoured to be the name of Dave Grossman's character in RPGs.