Processes can easily be filtered by user. In htop, press
u and select a user name, or run
htop -u $(id -un). You can also make other users' processes visible but grayed out by ticking “Setup → Display options → Shadow other users' processes”.
The “desktop stuff” are processes running under your user. There's no concept of “process that's part of the desktop stuff” vs “process that's an independent application”. As far as the operating system is concerned, the parts that make up the “desktop stuff” are applications like any other. The definition of “desktop stuff” vs “other stuff” is purely arbitrary. A program launched manually by clicking on an icon is indistinguishable from a widget that was started automatically at the start of the session.
If you run programs from a terminal, you can run the
ps command in a terminal. By default, it lists only programs started from that terminal.
While you could list all the programs started from any terminal, that wouldn't be meaningful, since it wouldn't include programs started from a desktop menu or icon.
If you're only interested in GUI programs that aren't part of the desktop, listing windows would be more meaningful. Try