@Snatch: there are various ways to go about it..
MBR Analysis..while computer is on from usermode or kmode..This also can also be done while Hard Drive is 'dormant' by attaching it to another computer and doing Direct low level disc scanning.
Also as Woodmann stated if you can get a application running before the bootkit you can detect it

its more a ring -1 or HyperVisor solution,some ASUS motherboards have a Linux OS that run straight on the Motherboard..but then this also opens up the vector of attack directly to the motherboard.
But these solutions are all just band-aids for after the fact infection detection.. I am more into the idea of before the fact infection prevention..as most rootkit and bootkits come with some 'installer'..I use the word 'Installer' lightly because It could be a true 'Installer' or it could be a exploit install..the regular installer method more then likely requires Administrative Privileges to write to the MBR..the Exploit Install method only require that the user that is under attack by the exploit be a Administrative User or uses some for of privilege escalation.
But both methods have alot of things in common..
Both have to use NtCreateFile or NtOpenFile to gain access the Hard Drive
Both have to Read From and Write to the MBR..NtReadFile NtWriteFile..
Both have to place Files on the Disc...so that the bootkit actually performs its duty..
Both have to Gain Execution of a Thread at some point to do all or most of this work for them..
Regards BanMe