Tools and materials
1. Whatever you want to use as a case. In this article, I am using a slightly modified tool case.
2. Foam. Textile store sell it and it is ratehr cheap; I got two 40cm*40cm*3cm blocks for 1,50€ each.
3. A steel ruler for the measurements. The steel ruler works best in this case because we are going to mark and cut the foam later on and a steel ruler can provide necessary guidance.
4. A sharp knife and a pair of scissors to cut the foam.
5. A felt-tip pen to draw on the foam

Preparations
This is what I am using as a case: An old tool case. A simple thing really:

First of all, I'll have to modify it a little. There is a "hang-in" compartment that I cut off and glued to the back wall. It will contain rulebooks and general sheets of paper in the end. Then there are two little plastic angles that held that compartment. I loosened the glue under them by sliding a craft knife under them and wiggling a little, now they can be freely rotated. I can rotate them downwards to hold two lyers of foam in place or rotates them up to make way for a third layer, so just as the need arises I can modify the storeroom my paper compartment and my foam compartment has to offer.
Them the actual part that is supposed to take in the foam. I made two parts: the right will usually hold my miniatures, the left will hold either any larger books (for roleplaying games that need less miniatures and more written material - it is just a tiny bit wider than A4 standard) or even more foam to put miniatures in (for miniature games). After those really simple alterations, that is what my case looks like from the inside:

Measuring and the mathematical part
Now don't sigh, the mathematical part will be easy
First of all, we'll need to measure both compartments. Coincidentally, the right compartment is 21cm*31cm and the left one 19cm*31cm which leaves me with only a 9cm*40cm wasted strip from each block. Lucky me!
Now that you know what you'll be working with, decide on the size of the mini compartments or decide how many miniatures you will want to have per row and column. This is where the mathematical parts comes in!
Personally, I decided on a compartment size. I chose 3cm*5cm, which seems to be a very good choice as most minis fit there. Now we also need to decide how thick the walls should be that seperate the miniatures. Personally, I took 1cm across and 1,5cm top to bottom, but you might want to double that; it seems a little flimsy now that I see it "in the flesh"
Now here is our formula:
M = (F - B ) / (C + B )
M is the number of miniatures per row, F is the foam width, B the width of each wall between the minis and C is the width of the compartments themselves. Confused? It's really simple, let's take my case for example: The foam is 21cm wide, the walls are 1cm each, the compartments are 3cm:
(21 - 1) / (3 + 1) = 20 / 4 = 5
Now I know I'll have 5 miniatures per row.
Play around with the numbers for a while until you find a good compromise between strength and number of compartments. Do the same for columns then.

As I said, it's simple. You should now have a very good idea of what your foam should look like later, time to mark and cut!

Marking and cutting
Now that you know what you need,mark your foam! Lay down your steel ruler, try to get as good a 90 degree angle as possible and mark away. You're not destroying anything yet, so errors are not a big problem. You need to use a felt-tip pen though as most other markers will get tangled in the fine structure of the foam. My foam looked like this when the first piece was marked:

You do not have to be exact to the millimeter, as the foam will give way without much of a problem, however do not stray to far! After you have marked the outline of your case, get out your ruler again and mark the compartments, taking care to be pretty exact. In this picture, I ahve already cut out the compartments, sorry, forgot to take a picture before, but you can still clearly see my markings:

I kept one edge of the foam a little thicker to provide better stability in the end.
When you're done, the task gets even more mindless with just cutting out what you marked... use your steel ruler as a guide and cut the foam. For the compartments, I cut the foam along my markings, taking care not to go to deep, and then used a pair of tailor's scissor to cut off the foam cube from the actual tray.

Basically, you're done now! Here is a final picture of my foam tray holding some Confrontation minis:

Over the final layer of foam containing minis, I put another layer to protect my precious pewter beneath. It works well: I kicked the case for some time and nothing happened to my minis at all (Do not attempt at home).

That's it for now, later on I will continue this article with guidelines to prettying up the foam tray and some other nifty stuff I plan to add to it.