I only use three graphical apps: Firefox, pidgin (grudgingly), and the Qt interface for VirtualBox. The rest are text apps and custom shell scripts for accomplishing tasks in tandem with those apps (such a "find | random | mpg123" for shuffling music directories).
I highly recommend "evilwm" for managing such a setup. Its single-pixel window borders with no window decorations is desktop minimalism as its finest. It's also got the lightest memory footprint of all the minimal WMs out there. Windows can be moved, re-sized, and snapped to locations with keystrokes. For fine-tuned placement of regularly-used apps, a simple shell script can be crafted to launch them with the precise geometry you require (or ALT+MOUSE_LEFT to lift the window). I have hot-keys defined (using "xbindkeys") that will populate virtual desktops to exact specifications.
My only gripe with this setup is the competition for key chords amongst emacs, screen, and evilwm itself. That, and every once in a while, some web page will throw a Firefox window that I simply cannot close without the "x" screen decoration (at least not without closing Firefox itself -- grrr...).