Spent the last two years designing mine.
My problem is too many hobbies: Wood working, Chemistry, Light metal working, Robot building, Electronics, computers etc.
Never enough room. Need lots of storage.
Build it twice as big as you need. I settled on 60' x 100' two story pole barn. Then got laid off, so not building it. (yet)

Make sure you have an office, place to design, relax, meet with friends

Woodworking make you put in a dust collection system, DIY design out there, for long term health.

Design it for solar heating and power from the get go, the overall cost is minimal over standard construction. Low cost methods at www.builditsolar.com
Make the solar heat collector the roof.
Consider papercrete for the walls.

Even my wife comments that on a sunny day its the best place to be in the house.
Lighting is really important, and natural lighting is be best.

The other thing that I like a lot is the carpet floor.  Seems a bit goofy, but its very nice to work on.  The carpet is left over from reflooring the living room, and is not permanently attached to the floor.

Enough electricity, natural light and powered ventialtion to allow welding indoors if it's not possible outside.

A strong shop wet/dry vac, brooms, shop rags and compressed air to keep things clean.

Large sturdy wooden and metal top tables with bench vises on them.

 For a fridge use a ammonia abosrbant gas fridge and make ya own wood gas to run it. That will work in colder climates but forget it when it 40C+ in the shade. I know as I'm finding that out now after 5 years of running one.

Personally, I will have a suspended floor I work on. And - it will probably be 'heated'. Life is a lot better in the Winter when one's feet are warm.

Outlets, cable TV, telephone, etc.  Maybe Cat5.
Cheap, quick, and easy to do before insulation and drywall.  Not so later.
I still have 1 spare cable TV wire and 2 spare 110V wires from the basement to the attic, not connected on either end, but available should they be needed.

Insulate inside the concrete block before they cap it.
Insulate the hot water pipes inside the walls with those foam tubes.

Man, I wish I had:

Thicker outside walls, for more insulation.  My uncle just built a house.  2x6 walls added only $900 to his total cost (lumber, insulation and labor), and it would have been less but his wife wanted 9' ceilings.

Pipes in the cement floor(s), as others said.  Cheap and easy to install before pouring, even if you never plan to use them.

An intercom from the workshop to living area.  We use cell phones.

A "shower drain heat recovery device".
http://www.fieldlines.com/story/2007/12/13/172543/25

I'm converting some old horse stables into a workshop so I have been thinking a lot about those things too.
For the electricity:

Put some PVC pipes in the floor. This will come in handy if you want to place some extra cable across the shop. If you do this be aware that this isn't good practice if there are a lot of mice or rats around.

Use protected lighting. I would have broken a lot if I didn't had a cap on mine.

Some other handy things to keep in mind:

If you work a lot with iron bars, make sure that you have a good place ware you can store the standard length of iron bars (here it is 6m). Otherwise you will have to cut them every time you want to store them

So to recap:
*    Double the Space you think you will need.
*    Oversized conduit in walls and floor for future modifications to wiring
*    PEX pipe in the floor for heating
*    3/4 bathroom
*    Oversized Doors
*    Workbench and cabinet space at your personal height.
*    Proper Ventilation/Dust Collection System
*    Proper Insulation, Window placement,
*    Design with RE in mind for power

Insulate under concrete slabs, and install well insulated roll up doors in shop/garage.

A kitchenette setup on wall of shop backing to the bath allows for short utility runs - think slop sink, counter, and range (oven for powder coating, burners for other stuff). And as others have commented - mini fridge, coffee maker, microwave.

A separate parts room allows for organization and keeps everything away from sawdust/welding smut. It also allows for somewhere to put a compressor that would keep the noise down.

If the ground slopes off I have seen (and plan on doing next time) a roll up door out one side of the shop leading to a patio/outdoor work area/loading dock. this allows for easy (and sometimes lower cost) deliveries, and less stress loading items going out.

Long power strips (like plugmold brand) on walls above benches or on the edge of freestanding work tables makes for easy power access.

Wire for 20 amp circuits - It uses 12 gauge instead of 14 Gauge and allows for heavier duty tools.

use spec grade switches and outlets - they are designed to last through many more cycles.

We're a little above 10,000 feet elevation in the Colorado Rockies.  The lowest temp I've seen here in 5 years is -15F.  Usually during winter the temps range between 3F and 20F.  The house is 375 square feet inside, basically a greatroom with a kitchen and bathroom.

Our foundation is a concrete slab.  It was poured inside ICF's.  Below the slab is 2" of styrofoam insulation.  The water lines are about 4' below that and have another 2" of styrofoam on top of them.

EVERYTHING in the house that is electrical runs on 12vDC, with one exception that will soon be remedied (a heating device for our on-demand water heater).  We have full 120v available inside when we want it, basically we use it to recharge cellphones and run a hairdryer occasionally, that's it.

The lights are 12vDC, using standard household fixtures and socket converters that let us use automotive bulbs.  The water pumps are Shurflo RV pumps.  The refrigerator is an Isotherm CR90.  The on-demand hot water heater is a PrecisionTemp RV-500.  Heat is supplied by an Empire DV-35 propane heater that is thermostatically controlled but requires no electricity, its pilot light heats a thermopile.  We also have a Jotul F100 woodstove.  Insulation is R19 in the walls, R38 in the ceiling.  We went for a cathedral ceiling to make it feel roomier, and it does.  During winter when the temp is in single digits outside and we fire up the woodstove, we have to open windows to keep from getting run out of the place, an inside temp of 80F+ is almost too easy to achieve and it's taken some practice to learn how to keep it reasonable.

There's a 12v control panel in the kitchen above the range hood inside a cabinet.  On average the house runs at maybe 4amps.  The 12vDC isn't really 12v, it's really 13.7v provided by a Samlex switch-mode DC converter attached to our 24v battery bank.  So we're talking about an average power usage for the entire house of maybe 70 watts.  When I run my laptop it's about 60 watts by itself but a lot of the time the house is drawing zero current.

About 12' from the house is the generator/power shed.  It's about 6'x12' in size, the south half is the electrical room and the north half is the generator room.  They are separated by a wall that I made as airtight as possible.  The generator room has never yet been used for a generator, it's currently full of "stuff" we have no other place to store.

The electrical room contains a battery box made from a large plastic tub turned upside down and vented through the roof with 4' poly pipe.  It has room for just 4 batteries, and I may replace it this summer to expand the battery bank.  Currently the battery bank is 250AH.  It's connected to a Xantrex DR2424 charger/inverter, a Samlex SDC-30 switch-mode voltage converter to provide 12v, an Outback MX-60 solar controller (currently acting as a costly voltmeter as I've no solar array yet), and a meter/switchbox for an AirBreeze wind turbine.

The power lines between shed and house run underground.  There's also a 1" poly pipe that's there for possible future instrumentation inside the house.

I *should* have run a second line between the power shed and the back of the woodstove so I'd be able to conveniently run a line from some kind of heat-powered device, but I failed to do that.

Currently we charge the batteries from a gas-powered generator which runs a few hours a day.  The wind turbine helps out but was never intended to do the full job, just add a bit during blizzard conditions.