For the "low-end" market:
SGI was dying because of hardware, and Linux couldn't save them. Their MIPS processor was surpassed in performance by Intel and AMD, PCI-X and Hypertransport cut into their high-bandwidth bus advantage, and commercial graphics cards got good enough to kill their graphics advantage.
Maya getting ported to Windows, Mac and Linux on the now quite fast commodity hardware didn't help either.
Then SGI came out with Windows workstations, but Microsoft ceased supporting their hardware after Windows 2000. This flirting with Windows was a major financial loss and big part of their downfall (there you go, if you want some OS blame).
Then they decided to go with Intel's Itanium, which was like a drowning person asking to be rescued by the Titanic years before it even sailed.
It's too bad, because they made some sweet machines in the day. Their flat panel display is still in demand despite being several years old:
For the "high-end" market:
Their big iron is doing okay. Linux helped because current Linux apps can be run on their hardware, and they don't have to pour so much into IRIX anymore (in fact, the latest incremental updates to IRIX cost money).