True Crypt supports disk based encryption too. However, that would means that the host system needs to have True Crypt before it can open your encrypted disk. I would prefer another way to install that. Instead, you should download True Crypt and expands all the files into a folder or the root directory. Then create a file based encryption with the remaining space. In this way, you will be able to mount your encrypted file with the True Crypt binaries in the main directory on any machines. So, make sure you get all the version of True Crypt. For mac and linux as well if you want to mount the file there. You can also upgrade true Crypt easily this way. This give you truly independent OS portability especially on your PenDrive and Portable HDD. Unfortunately, its easier said than done. I probably wont go make a mac + linux binaries anyway, since they vaires so much.
Now, lets talk about the failing of this. True Crypt can fail in some ways. For example, you forget to eject the thumbdrive and pull it out. Or if you crashed Windows with a blue screen halfway writing to the Thumbdrive. Or the Thumbdrive simply goes dead. One solution for all 3. Backup. You can backup the raw or the encrypted file itself. Of course, there are ways to avoid issues especially from the first case. When you mount the file in True Crypt, choose the mount options and check mount volume as removable media. The 2nd and 3rd case is a bit hard to avoid, but do you know that there is rescue disk for True Crypt. This only applies if you encrypt the system partition though. Mount you file for the first time, select system->create rescue disk and follow the instruction. That proves to be a life saver sometimes in the 2nd and 3rd case. But in the case of a removable drive for True Crypt, this does not apply at all.
Well. The autorun.inf you will need to make the automount and dismount for hte thumdrive is as follows :
action=Mount TrueCrypt Volume
Just copy and paste the above into notepad and you need to edit
That was the old days way fo doing it. Now, just install and run Tools->Travellers Disk Setup and you will be guided with a wizard to creating the above. That takes all the fun away does it not...