I use OnMyCommand extensively, and most of my commands execute silently (the Terminal isn't used). There are some, however (top -u, for instance), that must be executed in the terminal.
Problem: I prefer iTerm to Terminal.app, but OnMyCommand sends everything to Terminal.app.
Solution: iTerm's extensive AppleScriptability. Using OMCEdit, you can modifiy any command that executes in Terminal.app to execute in iTerm instead. Just use the following code:
osascript -e 'tell app "iTerm"' -e 'activate' -e 'set myterm to (make new terminal)' -e 'tell myterm' -e 'set mysession to (make new session at the end of sessions)' -e 'tell mysession' -e 'exec command "/bin/tcsh"' -e 'write text "INSERT SHELL COMMAND HERE"' -e 'end tell' -e 'end tell' -e 'end tell'
Replace INSERT SHELL COMMAND HERE with your command (top -u, for instance). You can also use any of OnMyCommand's objects (cd __OBJ_PATH__; ls -la, for instance).
One final thing to note: Make sure to set Execution Mode to "silent"; otherwise, a Terminal.app window will open to process the osascript, thereby defeating the whole point of this hint.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20030609222910699