If a machine is hijack by an hostile entity, then the attacker can gain full access to the hardware -- including every drive which is currently plugged in the machine. If the Linux drives are encrypted with a key that the Windows system never sees (which means that if you want to copy files from the Linux to the Windows, you have to do it from Linux, not from Windows), then such an attacker should not be able to read your Linux files. However, he can still do some considerable disruption.
Moreover, a boot disk is never completely encrypted, since at least the decryption code will be stored "as is". An industrious attacker, who gained control of your Windows machine, may plant some hostile code in the boot sector of the Linux system, so that it grabs a copy of your TrueCrypt passphrase the next time you boot Linux. Of course we are talking about a competent attacker here, but such people exist.
Apart from disks, the BIOS is commonly a re-flashable chip, and thus may serve as vector for hostile code. BIOS virus exist. Other pieces of hardware also have firmware, to be executed by the main CPU or even hardware-specific CPU, and such firmware may also be infected (this has been demonstrated in lab conditions, not sure it was spotted "in the wild"). If a machine is compromised, the compromise can go deep... But then, the attacker is really good, and really hates you, personally.
A "complete" solution would be virtualization -- the VM layer offers only virtual hardware to the potentially infected OS, keeping the rest of the machine clean. However, this is relative to how well the hypervisor can contain hostile code; hypervisor bugs occur (not often, but still...). A bigger problem will be that games will need some rather direct access to your GPU. It may not work at all, or imply heavy overhead; it may also provide an escape route for the attacker. After all, the GPU can run code and has privileged access to the main memory bus.
In practice, isolating the Windows OS in a VM will not provide absolute security, but it ought to block the not-so-good attackers (e.g. mindless malware), and may slow down the best attackers. I am not sure about the compatibility of games with virtualized GPU, though.
A much cheaper alternative, which does nothing about BIOS/firmware hacks but will protect your disks, is to make you Linux disks external. Just unplug them before booting Windows. If they are not in the machine at all, they will remain safe.