I'd like to point out that having random programs scatted across external HDDs is an anti-feature to me. I never remember which files are where as it is. And too easy to screw things up by unplugging the drive...

Nevertheless it can be done - if you are dedicated, recompile the program with the prefix changed to the mounted root of your separate drive. Presto, automated installs to your external drive. Now, linking up all the bits can still be a right headache, but this is just a bigger nightmare on Windows (what will you DO if your drive letter changes?? You mean I don't have any system to automatically link up random programs on random drives which may or may not be present. Gosh darn, that package manager sounds like a good idea now...)

If you're using a laptop, you're probably due for an upgrade in HDD capacity, or if you're lucky enough to be on Desktop I'd recommend a board with hotplug capability and using LVM. I think no matter your platform you're going to have a hell of a lot of problems doing things your way. If you can patch the package manager to be able to do this, amazing! I don't think any system exists like this, period.