I am trying to create a multiboot flash drive, but I don't want to use fat 16 due to the huge performance cliff between fat 16 and other file systems like ext 2 or NTFS. I need to have multiple linux distrosl on my flash drive and choose which one I want at boot-time (preferably grub2) All of the tools I found online require you to use an existing fat 16 partition.
Linux – Create a multiboot USB drive with NTFS or ext2
ext2linuxmulti-bootntfspartitioning
Related Solutions
First, for using bootable CDs you don't need multiboot, so this is a part that I don't understand.
Second, why not put all the sensitive data in one encrypted truecrypt partition that you can open from whichever OS that you boot from.
Third, if this is company data you are protecting, you could maybe justify buying hardware encryption such as Apricorn Aegis Secure Key, or Imation Defender F200 Biometric Flash Drive.
From the Wikipedia article on UEFI:
The UEFI specification explicitly requires support for FAT32 for system partitions, and FAT12/FAT16 for removable media; specific implementations may support other file systems.
Personally I've yet to encounter any motherboard manufacturer who has implemented NTFS boot support in their UEFI modules.
Update: As mentioned in the comments below, two years after I posted the above there are now at least a few motherboards available with UEFI NTFS modules.
Best Answer
As I understands your requirement for a solution: You want a bootable usb stick with multiple linux distros on it.
You can solve this by using grub2, gparted, and dd/unetbootin.
1: format and partition your usb drive to the fit your distro needs
2: install grub2 on your usb device to enable distro selection on boot.
3: copy/install distros into partitions.
I did a similar thing a while back: https://github.com/magnuskiro/grubRescueDisk (I see that the readme needs some work, but at least you should be able to find something useful through the references.)
I have multiple (4 I think) partitions with different linux live images available on a usb stick.
I formate each partition with gparted and used grub2 as a bootmanager to select distro on boot.