We base our jobs on a $180/crew hr (2 man crew with truck/chipper and all gear). Doesn't matter whether the job is climbed, or use the bucket it's based on $180/crew hour. If we need 3 men then it's $270/hr. More equipment means the job is done quicker.
You also have to remember that you time will include travel to and from the job site, site set up (signs, cones, plywood if required etc), pre job paper work (we are legally required to do a prework job plan which include identifying hazards and work methods to overcome those hazards) and clean up.
$50-75 to drop a tree. I won't even drive to the house for that.
Unless the job is for a house being torn down and redeveloped, we always chip brush and clean up. Leaving debris to allow the homeowner to clean up at their whim is a sure way to get a bad reputation for doing a poor job. If the home owner doesn't want the job done properly, they can hire a hack, we're pros and expect to be paid accordingly. And yes, we get our rate.
If you are using Quick Books or equivalent, you can just use their standard invoice or create your own. What would be more important is to create a proper quote sheet/contract, complete with a unique identifying number. We don't do any work without signed authorization. The easiest way is to have a section in the quote sheet where the customer can sign. We'll also accept email authorization. Your invoice can then just refer to the quote sheet identifying number.
There are some images of people's quote sheets on the site. A standardized quote sheet also allows you to put all the necessary legaleze on it. You should run yours by a lawyer before using it.