If you want to do click tracking you'll have to replace all links from your message with links
that point back to your tracking script.
To do efficient tracking that you can actually use later for segmenting your list and better targeting you would have to track the subscriber's id and message and/or campaign id.
Some email marketing systems even track the link position in the message so you know exactly if the recipient clicked on the same link that was at the top of the message or in the middle and in the system that I have built I even track if they clicked a link in the html part of the message or the text part.
The tracker script would record all this information then redirect to the actual link.
Bounce tracking is done by processing the bounce messages that your server will receive or generate when a message cannot be delivered. I recommend using VERP: http://en.wikipedia.org/wiki/Variable_envelope_return_path
Open tracking is done by including the image with tracking code in the url. This would normally point to a script on your site that would record the subscriber id and message and/or campaign id then output the binary date for a transparent 1x1 px wide gif.
You can also track messages that are flagged as spam by some users of some ISPs like hotmail, yahoo, aol, and a few others. they offer feedback loops so every time someone clicks that "Spam" button in their webmail application they will send you a message that you can parse and determine the subscriber that actually flagged the message as spam. VERP also helps with this because the feedback loop messages don't always include the actual email address of the subscriber so you need another way to identify them. This page on wikipedia has a list of feedback ISPS that offer feedback loops : http://en.wikipedia.org/wiki/Feedback_Loop_%28email%29