Check out xclip. It allows you to move text, or files to the clipboard from the command line.
EDIT:
There are command-line screenshot apps discussed in this post: http://www.linux.com/archive/feed/57772 including scrot. This is from the scrot man page:
scrot is a screen capture utility using the imlib2 library to aquire
and save images. scrot has a few options, detailed below. Specify
[file] as the filename to save the screenshot to.
One last option is to find an X app which just takes a screenshot when clicked (no prompts, dialogue boxes etc), assign it to a hotkey combination and use xdotool to simulate that keypress from the command line??