Posting your system specifications would help. :P
Defragment your hard drives and scan for all viruses, spyware and adware. Disable as much as possible via msconfig and check your processes in the task manager, take screenshot, and if it's not too much trouble, post the screenshot here.
The problem is probably locating the boot sector though. Basically, upon boot up your system will scan all devices in a specific order (managed through the BIOS), and will boot from the first one it finds. The more drives and boot devices your system has to wad through, the longer it will take to locate the boot sector.
I'm not exactly sure how you would correct this problem, you could try eliminating as many boot devices as possible that you don't need, but the only other thing I can think of is simply keeping your drives as clean and organized as possible so that your system can locate the boot sector faster.
Intel C2D E6320 / AMD Athlon X2 3800+
Gigabyte 965P DS3 / DFI nF4 Ultra-D
2GB OCZ Gold PC2-6400 / 2GB OCZ Gold PC4000
eVGA 8800GTS 320MB / eVGA 6800GS 256MB
150GB Raptor / 74GB Raptor
2x500GB / 320GB
OCZ GameXStreme 850w / OCZ StealthXStream 600w