I have noticed that it took exceptionally long too boot into Leopard for some reason. It would seem to hang after the white background with the Apple logo but before the login window. It would just show a blue screen.
I noticed my external 2.5″ HDD’s LED was on constant red meaning it was being accessed so I pulled the USB from the MacBook Pro and it would fade to a light blue screen but still hung. After restarting I did a couple of tests with the HDD plugged in and unplugged.
I can conclude that it would seem to be the HDD. Some searching reveals that it would “check” the drive along with the internal HDD making it longer. A bit annoying if I had a desktop Mac and if it suffered from the same thing.