I like the low tech ways the best. I made a folder /.Tr in my home directory by typing:
$ mkdir ~/.Tr
and instead of using rm to delete files move those files to the ~/.Tr directory by typing:
$ mv fileName ~/.Tr
This is an effective and simple way of keeping access to files you think you don't want with the added benefit in my case of not messing with the systems folders as my Ubuntu knowledge levels are fairly low and I worry about what I might be screwing up when I mess with system stuff. If you are also low level please note that the "." in the directory name makes it a hidden directory.