I have a few apps (such as Aisleriot) that are GNOME based, therefore they use the gnome defaults (which is some light theme), but I use xfce4 with compiz. My xfce theme is a dark one (atolm to be exact). How do I make the theme for these GNOME applications the same as my xfce4 theme? I already tried starting in gnome, setting the theme then switching back, this doesn't fix the problem.
If you set change the theme from xfce settings it should affect all GTK apps, including GNOME ones. There was a bug that got fix a while ago in which xfce couldn't set GTK3 themes properly. Otherwise it could be because you're using an old version of the theme which doesn't support GTK3. See if updating xfce or the theme solves the issue.