I have two taskbars in my current theme; the "usual" one for a normal number of tasks, and a "tiny" one for those occasions when I'm running software that opens lots of windows. I swap between them like so (triggered by exceeding the wrapcount):

tskBar1OnLineAdd !execute [!xTaskbarHide tskBar1][!xTaskbarShow tskBar2]
tskBar1OnLineRemove !execute [!xTaskbarHide tskBar2][!xTaskbarShow tskBar1]

You could also modify the taskbar sorting method on the fly (xtextedit?) and then reloading the taskbar.