As a Cognos customer I have asked this question directly to Cognos Support and more specificaly for Powerplay Enterprise server is it better to go for Unix or Windows plateforms.
The answer was that they do not recommend one plateform or another. They provide the applications for several plateforms ( hpux, aix , solaris, windows and some linux (redhat at least for reportnet and Cognos8).
According to them performance is the same regardless the plateform , everything properly tested and so on in their side.
One recommandation if you are starting with Cognos.
If you have only a Windows experience in your company stick to it, it will be too big step to start learning UNIX or linux at the same time, and vice-versa as well.
So considere also the in-house knowledge in Operating system you have, it will help a lot to fine tune the operating system to perform as well as possible with Cognos appli.
Now we have a mix of plateforms ( windows and hpux) depending on the application and of the need.
Reportnet in HPux in prod but in windows for test and dev, as hardware is cheaper for example