I have Linux on both my NDS and my iPod, one thing that stands out on both of them is that Linux boots basically instantly on them and I am trying to figure out why.

After POST and the bootloader, the standard Linux boot procedure seems to be 2 parts, one is the kernel boot and the other is the Distro's booting stuff, such as hardware detection, udev, starting other services and xorg etc. While this stage is probably mostly skipped on a device like the NDS the initial kernel boot isn't, and it takes a long time to boot on a powerful desktop computer but a few seconds on a NDS or other device.

These are not powerful devices, NDS has only 2mb ram and the iPods probably not much diffrent.

Is it possible to strip down a desktop kernel to be an embedded type kernel,
preconfigure the hardware as much as possible rather then rely on autodetection to get an instantly booting system (up until services load at least).

Both devices are solid state storage, but the Linux kernel is less than 2mb so it shouldn't take very long to load into ram. But I have heard of flash based booting systems such as IDE to SD/CF card. Why are these so much faster if it only needs 2mb of space for the kernel, it should be 3 seconds to read the kernel from disk and a few ms seektime?

The LinuxBIOS project for instance gets to a Prompt in less than 3 seconds, and the OLPC project boots in several ms.

Oh sure - the boot depends on what is going on and the micro devices have very little to do.

If you want to see some zippy boot processes for a PC - try the micro distros.

Damn Small Linux would boot most machines in under six seconds for eg.

You gotta remember that linux on a pc has a lot more to do on boot. Cut all those things out and it can be pretty instant.

Sure: customize a distro to your exact hardware.

Investigate The Linux BIOS Project.