What farm layout will produce the most chlorophyte?

As of 1.3, the rules for Chlorophyte spread have changed. There is now a limit of 41 blocks of Chlorophyte in a 95 block radius, so farms need to be much more spread out than previously. Neither a 5x5 nor a 3x3 farm will be optimal. If you want to do a rectangular farm, 6x7 is now the optimal size

My farm setup involves 2x 2x9 mud wells with one space between them.

╔═══╦═══╦═══╦═══╦═══╦═══╦═══╗
║ L ║ M ║ M ║ L ║ M ║ M ║ L ║
║ C ║ M ║ M ║ L ║ M ║ M ║ C ║
║ L ║ M ║ M ║ L ║ M ║ M ║ L ║
║ L ║ M ║ M ║ L ║ M ║ M ║ L ║
║ L ║ M ║ M ║ C ║ M ║ M ║ L ║
║ L ║ M ║ M ║ L ║ M ║ M ║ L ║
║ L ║ M ║ M ║ L ║ M ║ M ║ L ║
║ C ║ M ║ M ║ L ║ M ║ M ║ C ║
║ L ║ M ║ M ║ L ║ M ║ M ║ L ║
║ L ║ L ║ L ║ L ║ L ║ L ║ L ║
╚═══╩═══╩═══╩═══╩═══╩═══╩═══╝

L = Lizhard Brick C = Chlorophyte M = Mud

With 36 mud bricks and 5 chlorophyte seeds, this design maximizes space usage while making it convenient to mine. Using lizhard brick means that you can mine the mud wells with the shroomite digging claw without breaking your mold or worrying about mining the seed chlorophyte blocks.

This design is based on the design used by DicemanX on the Terraria Community Forums.

I'd say that 5*5 squares will be the best.

When you have multiple small blocks instead of 1 huge 50 * 50 block. You will get the most profit. Just make sure that the area you're building it in is well lit.

Also make sure that the area is deep underground.

"A good way to create a "farm" for chlorophyte is by making a 5x5 square of mud and putting one ore in the middle. It is wise to use 5x5 because chlorophyte only grows for twenty five blocks, and then stops growing. Make multiple of these boxes atleast 2 or 3 blocks away from each other, so you can get in and out of the farms."

For lay-out examples, see the pictures on the wikia about Cholorphyte.

From my own experience, I think 5*5 is better. The 25-ore limit is reached quickly if you use many 3*3 squares with one ore inside, while 5*5 is a little slower but produces more ore before reaching the limit. 5*5 has the extra benefit that you need less ore to set up the farm.