I have several somewhat separate programs, that conceptually can fit into a single project. However, I\'m having trouble telling Eclipse to make several folders inside a pr
You can have multiple source directories in a single project, but your description makes it sound like you want multiple sub-projects in a project, which eclipse doesn't allow (as far as I know).
If you really just want multiple source directories, where ProgramA, ProgramB, etc. contain only java files and nothing else, then you can do this relatively easy. Right-click on your project in the package explorer, and select Build Path -> Configure Build Path.... In the dialog that pops up, make sure Java Build Path is selected in the left pane, click the Source tab, then click the Add Folder... button. Pick ProgramA from the list, and repeat for ProgramB, etc.
If you want each source folder to have its own output folder, just check the Allow output folders for source folders checkbox and edit the output folders as desired.
If that is not, in fact, what you want to do, then another option might be to group your projects into a working set. A working set is not an UberProject, but it does help keep your projects organized in the package explorer.