If future upgrades are part of your plans, consider designing to a generic form factor. The site formfactors.org can help tremendously. ATX motherboards have a maximum size of 305x244 mm. MicroATX specifies a maximum size of 244x244 mm, and FlexATX specifies a maximum of 229x191 mm. The diagrams below should help you visualize the difference:

MicroATX compared to ATX

FlexATX compared to ATX
And as far as the AMD vs. Intel holy war, nothing I write here will change anyone’s mind so we’ll just move right along to….
Footprint
Just how big do you want your case to be? This really should be a reflection of the case’s purpose. A clear full tower with mostly empty space inside will look a little wrong to most folks, so save your grand designs for cases that are intended for watercooling or other esoteric purposes (or if you have a lot of hardware to cram in). Most case builders go for small, and it can be a challenge to your design abilities (and your budget) to see how small you can go.
Keep in mind that the material has some thickness. For example, using .250 inch material will mean that the inner and outer dimensions of your case will differ by half an inch. That’s an important factor.
The motherboard dimensions dictate minimums for at least two of your case dimensions. In practice, even those two dimensions will be larger than your motherboard by at least two times the thickness of your material (and maybe a little more). Which two dimensions is completely up to you. You can mount the motherboard to any of the sides of your case (or the top, I guess). For now, keep an open mind about that third dimension. You’ll be making other decisions that will dictate your minimum for it, starting with…
Drives
A system with just a hard drive can be useful if it’s connected to a network. A system that just has a CD-ROM drive can be a useful network appliance (firewall or router). But most of you case builders will want at least one of each.
With hard drives, shopping is quite a bit easier. The standard size for hard drives is relatively compact, and should stress your design much. You may even have room left over for a second one. Case builders in the quest for the smallest system can spend extra money on laptop hard drives, but it’s really a triple penalty: you pay much more for a smaller, underperforming drive. So if you aren’t trying for a size record, you can get a lot of ATA100 drive for $100. Variations in size among brands will be negligible.
CD-ROM drives pose a more interesting puzzle. You may want a slim CD-ROM drive for space reasons. Slim IDE CD-ROM drives can be as inexpensive as $40, with server-grade components costing more. You’re unlikely as yet to find a slim DVD-ROM drive without resorting to laptop components. Laptop drives are much less standardized, and you may be posed with challenges with connectors.
Beyond size, the other interesting aspect of CD- and DVD-ROM drives is the fact that the media is removable. Well, that’s obvious enough, but it implies that you will need to design a means for the media to get into your enclosure. CD- and especially DVD-ROM drives are available with slot-loading mechanisms instead of the older tray loading style. A slot-loading drive can be housed entirely within your enclosure (or ’stealthed’), with just a slot cut in the case to allow media to pass through. A tray loading design will require a cutout of sufficient size to allow the tray to open, and will be restricted to mounting positions in one or two planes. A slot loader may be able to be mounted ‘toaster-style’ as in the Apple cube (depending on the drive).
When it comes to floppies (do you really need one?), if you just can’t live without it, there are designs available that combine a CD-ROM and floppy drive into the normal 1.750″ height package of a CD-ROM drive. These are available from retailers that specialize in server grade hardware. You should consider just connecting a floppy on an ‘as needed’ basis, or using bootable CDs.
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