It depends on the size of your installer how you do things... Two of my products are small enough that I include ARM, MIPS and SH3 builds all together and the installer sorts out which to use.
It doesn't sound like that will be an option for you, I'm betting the executable and everything else is a fair size... I'm not sure what the acceptable cut-off really is, but I'd guess anything that someone has to download above about 2 megs you probably want to avoid.
If that's the case, separate installers is the way to go. As for configurations, SH3 is obviously dead, MIPS is still nice to support if it's not going to cause you any trouble. ARM is a given, and maybe you have an X-Scale-optimized version too.
As for OS concerns, I'm not sure you have to differentiate between them... You would be going by CPU type, either MIPS or ARM (and maybe an optimized XScale version). Since ARM could be PocketPC, 2k2 or uber-Windows Mobile Edition 3008 (or whatever it is now), you wouldn't go by OS I think. At least I never have.
