I installed (aware of the risks) software from the Elementary Team PPAs and I set up a Pantheon Shell session, which is based on Gnome. I would like to have Plank (a fork of Docky) to run at startup for this session, but not when I'm logging into Unity or the Classic Gnome session. Adding Plank to the Startup Applications list makes it run in every Gnome-based session. Thanks for your help!
Startup applications are defined by .desktop files that live in ~/.local/share/autostart, according to the Desktop Application Autostart Specification.
They optional setting to limit them to one or more desktop environments, e.g.
Alternatively you can use
to exclude this app from the listed desktop environments.
Only one of these keys, either OnlyShowIn or NotShowIn, may appear in a single .desktop file. (That was a direct quote from the spec.)
Unfortunately, I'm not sure what you're doing qualifies as a separate desktop environment...