Is it possible to enable TrueCrypt's pre-boot authentication with system partition not encrypted? I would like to encrypt only the other partition where I store data and I would like it to be automounted at boot time (not at Windows logon).
It is possible to automount an encrypted partition before Windows logon if you are willing to store password as plain text on your system partition. On the other hand, pre-boot auth in TrueCrypt is closely coupled with encrypting the system partition, so I'd say you cannot do what you want without modifying TrueCrypt.
If you consider going the former route, a simple one-liner such as
would do the trick.
Also, the performance hit from encrypting the whole system is not huge with TrueCrypt, especially with latest disk and CPU technology (SSD, AES NI instructions). Even on older hardware it is tolerable and at times unnoticable.