For GTK2 apps, the way to do this was relatively simple. You can launch a gtk2 app with a custom theme like this:

GTK2_RC_FILES=(path-to-theme) (command)

So for example, this worked:

GTK2_RC_FILES=/usr/share/themes/Redmond/gtk-2.0/gtkrc catfish

(Catfish is an app I know to be gtk2 -- you may not have it installed.)

Unfortunately, this feature broke entirely in GTK3. I can't gaurantee this will work perfectly, but you could try making simple shell scripts that configure a theme, launch the app, then unconfigure the theme. If you launch two apps at the same time, that my result in a race condition with unpredictable results.

So for example, you could launch gedit like this:

#!/bin/sh

if [ -h ~/.config/gtk-3.0 ]

  then

    rm ~/.config/gtk-3.0

fi

ln -s /usr/share/themes/HighContrast/gtk-3.0 ~/.config

gedit "$@" &

sleep 1

if [ -h ~/.config/gtk-3.0 ]

  then

    rm ~/.config/gtk-3.0

fi

Besides the race condition, doing this has some other undesirable side-effects. For one, you'll use more memory for each application that has its own theme. For another, you'll have to write custom shell scripts and launchers for each app. Finally, in my opinion, your desktop will look weird.

But there. That's how you can do it, sort of.