Not exactly sure what it is you're trying to do here but I have a couple of suggestions.
With the info in this thread you could WOL your PC from the PBO:
Wake up Windows Home ServerNAS from Mede8er
If you want your pc to do something when it boots up, I recommend AutoHotKey.
I found it very easy to use and therefore quick to do what I needed.
If you want the PBO to do something when it boots up, you want to look at editing /usr/local/etc/rcS
If you want to control the dvdplayer on the PBO, you have to append control commands to a file "/tmp/ir"
the shizzle mod makes the pbo start up in videowall by doing this:
/usr/local/etc # echo -n "D" » /tmp/ir (» means append to file)
/usr/local/etc # echo -n " " » /tmp/ir
so enabling "remote control" in the system menu means that you can send keystrokes into a "file" on the disk and those are passed to the standard input of the dvdplayer program like IR commands
D means move next
" " blank presumably means "ok" or "enter"
don't know what the other control codes are yet.