Unless you can remember exactly how things were placed within your computer prior to the suspected intrusion (a photographic memory, or a photograph, are two such tools that immediately come to mind), it will be very difficult to know if your hard drive was removed from your computer.
Note: Chassis intrusion features can usually be circumvented, so this may not be the most reliable method either although it can be helpful.
Chances are that an intruder who knows how to do this may also be smart enough not to modify your disk in any way, and either just copy only the files they want/need, or copy the disk in its entirety so they can "snoop around" at their leisure at some later time.
The bottom line is that if you're truly concerned about someone accessing your hard drive, you have to be preventive. If physically removing your computer away from the danger is not a viable option, then encryption works very well; this is my favourite disk encryption tool:
TrueCrypt (free and open source)
What I particularly like about this tool is that there's no built-in backdoor, so even a court order won't get it decrypted if you've taken the right steps to protect the encryption key.
How this tool is relevant to your situation:
If your hard drive is encrypted, and the intruder removes it from your computer for the purpose of accessing your data, they will only find encrypted data (and, initially, the Operating System will most likely detect it as an "uninitialized disk") that simply looks like random information to just about everyone.
The two ways the intruder may gain access to your data is:
A "lucky guess" at your password (so pick a good one that's difficult to guess, even with a brute force attacking tool) or key (highly unlikely, although not completely impossible)
You provided a copy of your password or key to the intruder (intentionally or unintentionally)