didn't you try
make ARCH=nios2nommu CROSS_COMPILE=nios2-linux-uclibc- -C ~/uClinux-dist/linux-2.6.x M=`pwd` modules
which you will need to compile device drivers
instead of
nios2-linux-uclibc-gcc linux-2.6.x/drivers/misc/hello.c -o hello -elf2flt="-s 4000"
which suits for user programm.
You will find detailed explanation in the kernel docs.
hope this helps, but i'm not a kernel crack
maybe you take a look at the nioswiki for the module programming example.
by the way let me ask you, what do you want to do?
do you want to write a device driver or a user program.