OK, my goal with this bench was to:

make it strong
use all 4 feet by 8 feet (actually 49" by 97") of one MDF board with virtually zero waste
keep it simple (dimensional lumber & lap/butt joints)
keep it inexpensive
???
PROFIT (ha ok, metaphorically speaking)

Step 1: The Design

To keep it simple the frame is from dimensional lumber and attached by lap and butt joints and I spent a good deal of time determining their optimal placement and making sure I'd have screws in the right places to maximize the strength and long-term durability of this work bench. Check out the pictures for details as it'd be too confusing to explain.

Design Notes

I intentionally placed the front 2x6 legs inside of the top frame so that I'd have a perfect rectangle on all edges of the bench top. This also means the top frame is flush with the walls where I placed the bench.
The shelf is not as deep as the top so that when you stand in front of it you won't hit your shins on the shelf
The are 4 legs so that the bench can stand on its own should I need to move it for any reason.
The overall dimensions for this bench are: 96 inches wide, 27.5 inches deep, 40 inches high. Make it as wide as is comfortable for your space, like in a kitchen: there's no such thing as too much 'counter space.'

Some math to determine the depth for the top and shelf
Whatever width your MDF (or plywood) is you'll want to find two numbers that have a difference of 7 and together add up to the total. Based on this you'll know where to cut (rip) your 4x8 piece in two.
For Example:
48" = 27.5" top + 20.5" shelf
49" = 28" top + 21" shelf

The reason for this is the "6 inch side" of the 2x6 is actually 5 1/2 inches and "4 inch side" of the 2x4 is 1 1/2 inches, which totals ... 7 inches. Hopefully from this explanation and the pictures you can decipher what I mean. I broke a cardinal rule of carpentry by not measuring first. I assumed the 4ftx8ft piece of MDF I bought was 48x96 but it was actually 49x97. I think they do this so that if you drop the MDF on it's edge in transport you can still strip it down an inch on any side.

Height
My 2 cents about how to choose the right overall bench height:

Your purpose for the bench - do you want things at hip height so you don't need to bend over? OR will you need to get weight/leverage with what may be on the bench top?
Obviously the answer to #1 changes based on your personal height.

I'm about 6' 2" so I choose a height of 40 inches (+MDF & Hardboard thickness < 1") which is right about at my hips and is perfect for my needs. The placement of the shelf depends on what you have to store. Find the tallest thing you may want to put ontop of or below the shelf and plan accordingly.

Step 2: The Materials, Etc.

As the title suggests the materials are quite simple:

2x4's, a 2x6, ~4x8 MDF board, 4x8 HDF/Hardboard, and wood screws to hold it all together. Plywood would be ok too instead of the MDF/HDF combo if that happens to tickle your fancy.

I prefer MDF over plywood because it's cheaper than most plywood, doesn't warp, and (I think) looks nicer. However, MDF doesn't hold up well to liquids or general 'harshness' which is the reason for putting Hardboard ontop. Plus, once the hardboard gets beat up, spilled on, scuffed, dented, etc. you can pry it off and put on a new piece for cheap!

Tools needed are also pretty lean:

Strongly recommended:

a drill with bits and such
some kind of saw

Helpful:

a level
clamps
saw horses

Step 3: The Frame

To assemble the frame I roughly followed these steps:

cut the 4 legs to length (40" or whatever you prefer)
cut the sides from 2x4 to the depth (minus 1.5") of your work bench top
cut the back from 2x4 to the length (minus 3") of your work bench top
clamp all those pieces together (or have someone help) along with the front 2x4 and set your screws - I used 8 screws per corner (2" or 2 1/2" screws - I can't remember)
then cut your frame pieces for the bottom
clamp those 4 pieces of 2x4 and set your screws
measure the length needed for the 2x4 cross supports for the top and 2x2 (or 2x4 if you want) for the shelf below
again, clamp and screw the cross supports

Depending on how much of a perfectionist you are you'll want to check for level at various points or at least position the shelf frame at the same height on each leg.

Step 4: Finishing Touches

Some last steps for the sake of documentation:

Cut out notches in your shelf to fit around the back legs
Attach the bench to nearest (walls) so it won't tip over
Attach your MDF pieces to the top and shelf (I believe I used 1 1/4 wood screws)
Attach the Hardboard to the top (I used brad / finishing nails)
Put the work bench to use!

If I were to do this over again I would perhaps cut half lap joints for parts of the frame so that there aren't any gaps around the edges, but that would require more time and precise cutting with tools I don't have and you may not either.

Thanks for reading! I'll try to answer any questions if I forgot some details.