This article is from the Food Preserving FAQ, by Eric Decker firstname.lastname@example.org with numerous contributions by others.
Make pectin. Use as few seeds as possible and crush none to preclude ingesting
alkaloid and cyanide compounds which are present in lima bean, citrus and apples
The pomace from apple crushing / pressing can be used to generate cider vinegar.
Compost is a great way to solve the by-product problem. Your garden will
benefit enormously in the years to come. Do make sure the compost works fully so
that the seeds are digested. Add a sprinkle of powdered lime to each layer in
the compost heap to assure strong action.
Ivan Weiss has some good words:
I don't mean to get into an off-topic thread, but it is inconceivable that
there would be enough pesticide residue in any fruit peels to withstand a
proper composting process. I can tell you this authoritatively from five
years of annual inspections by the Washington state Department of
Agriculture for certification as an organic grower. I compost anything
that will rot (within reason), and the state, which takes a whole lot of
core samples, has never found trace #1 of any pesticides on my place.