There is a program, with source code available, that securely wipes the MFT. The program is located at:
http://www.sysinternals.com/ntw2k/source/sdelete.shtml. While the program is not under the GPL, the source code is readily available for download and the authors of Eraser can review that to determine its algorithm and implement something similar in Eraser. With respect to the paging file, the best that can probably be done is to encrypt it using something like CryptoSwap Guerilla - which can be found by googling the filename. Regarding databases and other documents (e.g. Word temp files, etc) the best thing you can do is have an encrypted drive/virtual drive container and set directories in the respective programs to save temps on the ones on in the encrypted container. As to the registry, probably the best idea is to use a windows tune-up program that searches the registry for dead references and eliminates them. Someone also mentioned a method for rebuilding the registry in another post. Once that's done a freespace wipe would need to be done.
Needless to say, you still have a security concern in the hibernation file because anything that's in RAM is saved to that. I don't know if you can target the hibernation file after you wake the machine or if it gets automatically deleted and you would need to do a freespace wipe. My suggestion would be to turn hibernation off.
