As mentioned earlier, I've been using the RatPoison window manager, along with Trayer for my tray applets. By telling RatPoison to give give it 26px of space and not manage it directly (see my .ratpoisonrc below), they both work flawlessly together. However, other applications don't play so nicely with them.
The problem seems to lie with applications with unusual fullscreen modes. For example, YouTube's fullscreen videos appear underneath Trayer, obscuring the video controls at the bottom. Some fullscreen Wine games may correctly display above Trayer, but have graphical glitches in its 26px padded area, and do not allow mouse interaction there.
Unable to find a simpler solution, I wrote a small Bash script to toggle both Trayer and RatPoison's padding. When run, it checks to see if Trayer is running; if so, it kills it and removes RatPoison's padding. If not, it resets RatPoison's padding and restarts Trayer. This works quite well, can easily be bound to a RatPoison key combination (I use 'p' (i.e. ctrl+t, p)), and doesn't affect any running tray applets, allowing the padding to be toggled as needed.
#!/bin/bash #Toggle RatPoison's padding if ps ax | grep -v grep | grep trayer > /dev/null then #If Trayer is running, kill it and remove RatPoison's padding. killall trayer ratpoison -c "set padding 0 0 0 0" else #Otherwise, reset the padding to normal and restart Trayer. ratpoison -c "set padding 0 0 0 26" trayer & fi
#Trayer unmanage panel set padding 0 0 0 26 exec trayer #Tray apps exec wicd-gtk exec xfce4-power-manager exec volumeicon exec SpiderOak #Bindings bind c exec roxterm bind b exec firefox bind i exec xchat bind e exec thunderbird bind p exec ~/.rpPaddingToggle.sh bind P exec keepass #Use j & k to switch windows, h & l to switch focus definekey top M-j next definekey top M-k prev definekey top M-h focuslast definekey top M-l focus