Truecrypt has proven extremely safe and efficient for me, I use it on both my desktop and laptop for full system encryption. It's very well-written software and has never given me the slightest issue. (I donated to them too)
There are a few gotchas, mind you: If you boot from your Windows DVD, startup repair won't see any OS obviously. If you want to access it through the command prompt, you have to run Truecrypt in portable mode (say, from a USB stick) and mount the system partition before you can work with it.
It will also slightly complicate your backup strategy - if you image the running Windows system, the image ends up unencrypted. If you image the system offline (from a WinPE environment such as Macrium's rescue disc) you can image it encrypted but will have to image every sector, i.e. save a clone of the full partition into the image file.
Despite these issues, I think it's really worth it. Just takes a bit of planning ahead.