The biggest mistake people make is to close up dead air spaces, thinking it will remain cooler in the summer and warmer in the winter. Big mistake. All you are doing is making sure the moisture builds up in your crawl space, promoting rot, and creating a nice environment for termites. This space needs to be dry, and the best solution is to cover the ground with a poly sheet and open up the vents and keep them open year round.
The vents are there for a reason, and they need to be open as much as possible and unobstructed. Your biggest concern would be to make sure the joist spaces between the conditioned area and the unconditioned area are properly insulated with a vapor barrier toward the conditioned area (a conditioned area is one that is heated or cooled, depending on the season). Your water heater and furnace being in the space unprotected is not the best situation, but it would make sense to wall in the mechanical equipment, or insulate it to make sure the pipes do not freeze and you don't waste a lot of energy.
A very informative booklet is Oak Ridge National Laboratory's ORNL CON-295, Builders Foundation Handbook. It outlines best practices for many different foundation designs and practical and cost effective solutions.