From Data Quality functionality perspective, there are no differences. Based on your requirement and resource/infrastructure availability you can use either Linux/Windows.
The lack of OS Profiles is the only option I can recall which differs between Windows and Linux. So if you don't use or plan to use OS Profiles then it's personal preference.
May I add to Robert's remark: If your admins are (for example) seasoned PowerShell experts and they have to switch to Linux, they will have a very hard time moving on to Linux. The same is true if you try to force seasoned Linux scripters to move to PowerShell or MS-DOS batch scripting.
Also the security concept of Windows can sometimes make life hard for you. One typical example is the use of mapped network drives. They work fine in any CMD shell you open, but they cannot possibly work for Windows services: at the time when a Windows service is started, mapped network drives do not yet exist on that Windows system; meaning mapped network drives cannot be used by processes in the Informatica domain. At least I haven't seen anything like this work fine yet. So if you use (or have to use) any batch flies or PowerShell scripts which utilise mapped network drives, forget it; they can't be used by a Windows service.
Another example is that it does sometimes matter which user starts the Windows service and how. At my current customer we're moving our environments from one SQL Server machine for the repositories (domain and PowerCenter repositories in this case) to another SQL Server machine. During this process the whole domain must be shut down, changed, and restarted. In one environment starting the service via infaservice.bat worked; in the other four environments we had to reboot the server in order to restart the Informatica service on Windows, and no one can tell us why.
In short: the Windows security concept can sometimes play nasty tricks on you.
In earlier times Windows services were far less powerful and not as scalable as Linux/Unix machines. As of my experience this no longer holds true, Windows and the server hardware have become so powerful that from a performance perspective you usually won't find much difference. Personally I still feel more comfortable with performing admin tasks under Linux/Unix than under Windows, but then I'm not a seasoned PowerShell programmer, and Bash and Korn shell are very rarely available under Windows.
My 2 cents.