I’m not sure what you mean by this – I either boot WinPE (from which I can then start some other Windows installer – including XP, though for that I have to format the disk before starting the installer, and copy the entire i386 folder to the disk), or I boot one of the other things.

Windows PE boots just fine off FAT32, and my USB key is FAT32-formatted (same goes for Vista/7/8 install media – there’s no need to format the USB drive to NTFS first, you can easily keep it FAT32, and make it bootable with \boot\bootsect.exe; in fact, AFAIK this is the only way to make an USB key that can be booted in EFI mode).

I get the part where you boot certain OS from a subfolder. My question was more along the lines – you are already running the OS and the system is asking you “insert CD xxx”. How can you “select” the right contents? Do you browse through a subfolder on the pendrive?

Also my WindowsPE pendrives are all NTFS formatted. How do you “combine” NTFS usb stick with a Fat32?

I’m using syslinux as bootloader. Booting everything from syslinux is pretty simple – the only problematic part was getting both WinPE’s to work (I had to use bcdedit to make a boot menu for them, so when I choose winpe in syslinux, I’m then asked which one I want).

Thanks for reminding me of ESXi – I’ve got that, too. It’s not much of a problem either – copy files off the install CD to a subfolder on the drive, then edit boot.cfg to remove /’s (so that files will be loaded from the subdirectory instead of root of the drive). Syslinux 4 can run mboot.c32 directly.