The following is an excerpt from @Necere 's post detailing the different considerations for the NCASE microATX case project thread on HardForum. It's specific to designing a mATX case but much of the information is useful for anyone designing a SFF case.
To start off, this is a rundown of the actual dimensions of the major components. It should be understood that the case will be at least 10 to 20mm larger in any given dimension than the components take up, to account for the chassis and exterior panel thickness, screws/rivets/other fasteners, and to make component installation possible. It's not necessary to read all of this, but it's useful to have as a reference.
1. Motherboard
This is a microATX motherboard with two full-length GPUs (312mm, the maximum called for by the spec):
Note the board itself is 244x244mm, however the rear I/O shield extends a few mm past the edge of the board.
Compared to Mini-ITX, microATX is significantly larger:
The depth of the board is just as relevant as the height, since we're able to use the space formed by the front edge of the board and the end of the GPU for a front-mounted PSU, drives, or fan/rad:
This is put to use in many Mini-ITX cases, including the M1, but due to its increased depth microATX has much less usable space available.
Limiting GPU length wouldn't save much space, since mATX boards often have right angle SATA ports at the front edge, which need a good 30-40mm of clearance:
That brings the total depth up to about 285mm/11.2", which isn't far off the 312mm of a full-length GPU.
2. PSU
In regards to the power supply, the things to note are the space required by modular connectors, and by a right-angled power cable (if used). The former needs, IMO, a minimum of 30mm for a still-snug fit, though more is better, and 40-50mm is even more ideal. In the M1, SFX-L used in conjuction with a long GPU only has 20mm for the modular connectors, which by all accounts is a rather tight fit.
The right-angle AC cable adds about 20mm to the length, which is something to take into account for those layouts that require it.
Editor's note: The 20mm allowance for the angled C13 connector is based off the very short connector that Lian Li and SilverStone use. Off-the-shelf angled connectors are usually much taller. For just a few units, spares can probably be sourced from Lian Li, SilverStone, or even NCASE. SilverStone's OEM division can make a custom length cord but the MOQ is 1000 units.
3. GPU
The PCIe specification gives a maximum length of 312mm (12.28"), and a (PCB) height of 111mm (4.37"). Note the height doesn't include the PCI bracket, which adds 15mm to the overall height.
It's also important to take into account the PCIe power connectors, which are typically located at the top edge of the PCB. These are the same type of connectors used for modular PSUs, and have a similar space requirement. This means 20 to 30mm should be added to the PCB height to determine the actual space required.
Reference GPU designs (i.e., cards designed by nvidia/AMD and usually manufactured and sold by third parties), almost always conform to the 111mm height restriction, and rarely come close to the maximum length.
On the other hand, third party manufacturer add-in boards (AIB) frequently exceed the specification, especially the maximum height. It's quite common for part of the heatsink to overhang the top edge of the PCB, and occasionally the PCB itself will be taller than average, with heights in excess of 150mm in some cases (e.g., ASUS Strix, EVGA Classified). Note how much further out this places the PCIe power connectors:
Some designs incorporate a recessed cutout for the power connectors to mitigate some of the extra height:
However, some space between the edge of the PCB and side panel is still needed to allow for proper airflow. The vast majority of tall GPUs use axial fan type coolers ("open" coolers), which exhaust laterally in all directions (as opposed to centrifugal/blower-type cards, which exhaust primarily through the rear). Since these cards don't take care of their own hot exhaust, it's especially important with these types of cards to have good system airflow.
4. CPU cooler, rear fan
I'm including these together because they both affect case width, and designing for one essentially gives you the other:
The basic choice is between designing for 120mm/140mm-class, 160-170mm tall tower CPU coolers, which gets you rear 120mm exhaust fan support; or 92mm-class tower coolers (or top-downs), which only allows for a 92mm rear fan. Naturally, the former allows for better cooling - both for the CPU and for system cooling as whole - as well as much wider cooler choice. This also has an impact on maximum GPU height, with the 92mm-class only allowing for GPUs up to 140mm tall (and PCIe power connectors must be included in that height).
The difference between the two sizes is roughly 30mm of case width. Note that, again, the actual case width would be at least 10mm greater than the space the components take up.
5. Cable management
Cable management behind the motherboard is not free! Basically, however much space you want to have for managing cables will need to be added to the case width. 10mm will get you a minimal amount of room to run smaller cables, but don't expect it to suffice for the 24 pin motherboard power cable. 20-30mm would be adequate-to-roomy, but that's 20-30mm of extra case width.
Also worth mentioning is the additional height required if you want to be able to run cables through the gap between the motherboard and top or bottom of the case. Here again, the height needed depends on whether to allow for only thinner cables, or thicker ones as well. In some layouts, there will be additional height for other components anyway, so no height increase may be required.
To start off, this is a rundown of the actual dimensions of the major components. It should be understood that the case will be at least 10 to 20mm larger in any given dimension than the components take up, to account for the chassis and exterior panel thickness, screws/rivets/other fasteners, and to make component installation possible. It's not necessary to read all of this, but it's useful to have as a reference.
1. Motherboard
This is a microATX motherboard with two full-length GPUs (312mm, the maximum called for by the spec):
Note the board itself is 244x244mm, however the rear I/O shield extends a few mm past the edge of the board.
Compared to Mini-ITX, microATX is significantly larger:
The depth of the board is just as relevant as the height, since we're able to use the space formed by the front edge of the board and the end of the GPU for a front-mounted PSU, drives, or fan/rad:
This is put to use in many Mini-ITX cases, including the M1, but due to its increased depth microATX has much less usable space available.
Limiting GPU length wouldn't save much space, since mATX boards often have right angle SATA ports at the front edge, which need a good 30-40mm of clearance:
That brings the total depth up to about 285mm/11.2", which isn't far off the 312mm of a full-length GPU.
2. PSU
In regards to the power supply, the things to note are the space required by modular connectors, and by a right-angled power cable (if used). The former needs, IMO, a minimum of 30mm for a still-snug fit, though more is better, and 40-50mm is even more ideal. In the M1, SFX-L used in conjuction with a long GPU only has 20mm for the modular connectors, which by all accounts is a rather tight fit.
The right-angle AC cable adds about 20mm to the length, which is something to take into account for those layouts that require it.
Editor's note: The 20mm allowance for the angled C13 connector is based off the very short connector that Lian Li and SilverStone use. Off-the-shelf angled connectors are usually much taller. For just a few units, spares can probably be sourced from Lian Li, SilverStone, or even NCASE. SilverStone's OEM division can make a custom length cord but the MOQ is 1000 units.
3. GPU
The PCIe specification gives a maximum length of 312mm (12.28"), and a (PCB) height of 111mm (4.37"). Note the height doesn't include the PCI bracket, which adds 15mm to the overall height.
It's also important to take into account the PCIe power connectors, which are typically located at the top edge of the PCB. These are the same type of connectors used for modular PSUs, and have a similar space requirement. This means 20 to 30mm should be added to the PCB height to determine the actual space required.
Reference GPU designs (i.e., cards designed by nvidia/AMD and usually manufactured and sold by third parties), almost always conform to the 111mm height restriction, and rarely come close to the maximum length.
On the other hand, third party manufacturer add-in boards (AIB) frequently exceed the specification, especially the maximum height. It's quite common for part of the heatsink to overhang the top edge of the PCB, and occasionally the PCB itself will be taller than average, with heights in excess of 150mm in some cases (e.g., ASUS Strix, EVGA Classified). Note how much further out this places the PCIe power connectors:
Some designs incorporate a recessed cutout for the power connectors to mitigate some of the extra height:
However, some space between the edge of the PCB and side panel is still needed to allow for proper airflow. The vast majority of tall GPUs use axial fan type coolers ("open" coolers), which exhaust laterally in all directions (as opposed to centrifugal/blower-type cards, which exhaust primarily through the rear). Since these cards don't take care of their own hot exhaust, it's especially important with these types of cards to have good system airflow.
4. CPU cooler, rear fan
I'm including these together because they both affect case width, and designing for one essentially gives you the other:
The basic choice is between designing for 120mm/140mm-class, 160-170mm tall tower CPU coolers, which gets you rear 120mm exhaust fan support; or 92mm-class tower coolers (or top-downs), which only allows for a 92mm rear fan. Naturally, the former allows for better cooling - both for the CPU and for system cooling as whole - as well as much wider cooler choice. This also has an impact on maximum GPU height, with the 92mm-class only allowing for GPUs up to 140mm tall (and PCIe power connectors must be included in that height).
The difference between the two sizes is roughly 30mm of case width. Note that, again, the actual case width would be at least 10mm greater than the space the components take up.
5. Cable management
Cable management behind the motherboard is not free! Basically, however much space you want to have for managing cables will need to be added to the case width. 10mm will get you a minimal amount of room to run smaller cables, but don't expect it to suffice for the 24 pin motherboard power cable. 20-30mm would be adequate-to-roomy, but that's 20-30mm of extra case width.
Also worth mentioning is the additional height required if you want to be able to run cables through the gap between the motherboard and top or bottom of the case. Here again, the height needed depends on whether to allow for only thinner cables, or thicker ones as well. In some layouts, there will be additional height for other components anyway, so no height increase may be required.
