So after a mate a work started raving about Gnome Do I decided to give it another go, not quite remembering which I gave up with it last time.

Quicksilver is a program I've always installed first when using any Mac and Gnome Do is a very similar thing for Linux.

It wasn't long before I worked out why I had ditched it. I keep switching between window managers and seem to always end up back with pekwm. Launching Gnome Do in pekwm for some reason causes the "window" to end up behind all the other windows.

A quick RTFM later and I found the answer. In my ~/.pekwm/autoproperties I added:

Property = "Do,Do" {
ApplyOn = "Start New Reload"
Layer = "Menu"
Title = "^Do"
}

which forces it above all other windows.

With that sorted the only thing left is the occasional erratic behavior of the window placement, but I can live with that for now :)