Can I use the Nios II Eclipse S/W Debugger if I don't have the quartus project?

The direct GDB part is easy; see the nios2-gdb-server example in Chapter 4 of the "Embedded Design Handbook" (page 4-11 of the current PDF on the website).

As far as eclipse goes, assuming you're using SDK generated makefiles for APP/BSP, I do something like this:

- start eclipse with a blank workspace (no other projects in it)

- File->Import->NIOS II ... -> Import custom makefile for NIOS......

- navigate to the BSP directory

- give the new project a name name

- finish the dialogs

- repeat the Import... this time for the APP directory

After that you can rebuild the software and download through the GUI.

If you're not using NIOS SDK makefiles / normal build procedure, this wouldn't work.