I haven't had the pleasure of dealing with border agents, but I would assume that they'd leave you alone as long as everything looked normal at a casual glance.
A couple example suggestions for that:
1) TrueCrypt let's you change the bootup text, and can be set not to visibly show keystrokes when entering your password. This means that you can make it boot into what appears to be a standard "No operating system found" type error message, which will not react at all until you type your correct password and hit enter. Unless they're dedicated enough to examine the boot sector they wouldn't be able to tell that it's not just a corrupted drive. Toss an OS install disc in your bag for added realism.
2) TrueCrypt will boot from CD into an encrypted drive. Using this to your advantage, install a small Linux partition and set your computer up to boot into that unless the boot CD is inserted. Nothing suspicious at all remains on the drive except for a parition of apparently random data, which they'd have to be pretty suspicious already to even bother looking for. You could copy the TrueCrypt bootloader back onto the drive to boot without the CD for convenience if you're not going to be crossing borders for a while.
...And there are probably other ways. The TrueCrypt documention offers a number of suggestions on how to look minimally suspicious to suit whatever level of paranoia you may have.