Let me just say this, I am very OCD about my backups and how I use my machine in general. While time machine is ok for most, the way it is implemented is rather scary considering how HFS+ works with hardlinks. I have had my backups get jacked up on numerous occasions because of the sheer number of files and directories on my drive.
http://arstechnica.com/apple/2011/07/mac-os-x-10-7/12/
From the article:
"One particularly scary example is the implementation of
hard links on HFS+. To keep track of hard links, HFS+ creates a separate file for each hard link inside a hidden directory at the root level of the volume. Hidden directories are kind of creepy to begin with, but the real scare comes when you remember that
Time Machine is implemented using hard links to avoid unnecessary data duplication.
Listing the contents of this hidden directory (named "HFS+ Private Data", but with a bunch of non-printing characters preceding the "H") on my Time Machine backup volume reveals that it contains 573,127 files.
B-trees or no b-trees, over half a million files in a single directory makes me nervous."
To empty your trash with terminal type exactly what I said, "sudo rm -rf ~/.Trash/*" without the quotes and you will be just fine.