Where in an Eclipse workspace is the list of projects stored?

Windows:

<workspace>\.metadata\.plugins\org.eclipse.core.resources\.projects\

Linux / osx:

<workspace>/.metadata/.plugins/org.eclipse.core.resources/.projects/

Your project can exist outside the workspace, but all Eclipse-specific metadata are stored in that org.eclipse.core.resources\.projects directory As noted in the comments by tk421storm, and in Jeegar Patel's answer:

In order for manual changes to take effect, make sure to do File -> Refresh afterwards.

In Mac OS X, it is under

<workspace>/.metadata/.plugins/org.eclipse.core.resources/.projects

In Eclipse 3.3:

It's installed under your Eclipse workspace. Something like:

.metadata\.plugins\org.eclipse.core.resources\.projects\

within your workspace folder.

Under that folder is one folder per project. There's a file in there called .location, but it's binary.

So it looks like you can't do what you want, without interacting w/ Eclipse programmatically.