Cookies...

I am new to the net and everyday for sure, if you are here you will learn something different, or learn about something that results in a series of more questions. So I went to one of my 'fav forums' and posted this question. I was told that the question really didn't belong in that forum and I was directed to you guys. So here goes, I came across a vague comment that lead nowhere and everywhere: so below is the post that I submitted...

Why would a webmaster use an invisible cookie, on his/her affiliates accounts.
What can be tracked by using this tool? Why do TE's frown on invisible cookies.
A lot of questions I know, but I would like to learn as much as I can about
invisible cookies...