There are two ways that I know.
With the project selected, use the movement keys in Organize>Move>Move (Down/Right/Up/Left), e.g. ^⌘↓, ^⌘→, ^⌘↑, and ^⌘←. Outdent the project first if it is nested in a folder, then move it underneath the destination folder, then indent it.
A faster way would be to use this script that I cooked up using some tips from this thread. It asks you for the exact name of the folder (empty or populated) and then moves the project to the top of that folder. Change “beginning of sections of`” to “end of sections of” in the script if you want the project to wind up at the bottom of the folder. Add a shortcut to the script in either FastScripts or LaunchBar and you can launch it from the keyboard.
repeat
display dialog "To which folder would you like to move this project" default answer "Folder"
try
if the text returned of result is not "" then
set the theFolder to the text returned of the result
exit repeat
end if
on error
beep
end try
end repeat
tell application "OmniFocus"
tell front document
tell document window 1 -- (first document window whose index is 1)
set selectedProjects to selected trees of sidebar
end tell
repeat with anItem in selectedProjects
set theProject to value of item 1 of selectedProjects
move theProject to (beginning of sections of (first folder whose name is theFolder))
end repeat
end tell
end tell
