Make sure you reserve enough space in your design for storage and closet space. If you're closing off your furnace room, make sure the room is large enough to provide enough combustible air for your furnace and hot water heater.
If the room is too small, you may need to add a vent in a window, or find some other means to get air into the room. Consult a heating & cooling specialist to make sure.
Depending on how much of a pack rat you are, you may need to reserve about 15% to 20% of your basement square footage for storage. You don't want to make it so small that it spills over into your main basement area, but you don't want it so large that it encourages you to keep everything!
The original layout of your basement may help you make this decision, as the storage area may have only one logical place and size.