Cross-compiling for the Yun I use the OpenWRT toolchain. It works rather well. Just set up your environment variables, configure for the mips target and your working.
Native GCC on the Yun is really only for playing around or if you an amazing amount of patience. I got it working just because I thought I could.
I was able to compile a native mips avr-gcc toolchain for the Yun. I'm testing that out with Arduino Makefile. It's working well. It's not as slow as I was expecting and is very usable. I have my whole avr-tools setup as a nfs mount to the Yun and am satisfied with it. I was going to make it a package, but having it separate from the main root filesystem is much easier and to me cleaner.
As far as qemu virtual mips there are some decent choices. You can use the malta snapshot from OpenWRT trunk (Index of /snapshots/trunk/malta/). It's specifically for running in qemu .
There's also the yocto project (https://www.yoctoproject.org/)that is rather easy to setup by reading the documentation.