I learned that it in fact is possible (and done by some members here), to use Eclipse as an IDE for Linux application programs (with and without MMU). Eclipse can be configured to help with perform editing, "make"ing and debugging. Regarding debugging they say it's possible to do remote debugging via TCP/IP using the gdb stub provided with the distribution.
It's also known that debugging threaded application does not work correctly yet. AFAIK, it will be fixed for the MMU enabled branch, though.
The Altera NIOS2-IDE is of no use here. Eclipse needs to be configured separately to allow for compiling and debugging Linux user land applications.
-Michael