What size motherboard?
there is a constant pull for the desire to built this small, silent networked attached storage (NAS) or server that absolutely disappears in a closet or under a desk. while those are amazing, for people who have never had a server before or know they are eternal tinkerers, i would advise against this. strongly.
the number one thing i tell people who want to go with anything besides ATX is: servers are like goldfish – they expand into whatever size home you put them in. in other words, if you build an ITX server, you are only ever going to have ITX size expansion, which will keep you limited and small.
initially people built a NAS or a server for a single purpose, and because of this, realize they can get away with a small form factor (SFF) build. this assumes your build will ever only be used for one purpose and there is nothing in the future this computer you have will be useful for. anyone who has been in the server space for more than a month will tell you that you are only ever one youtube video away from desiring more from your hardware. not to mention your money.
the best recommendation for most people is to go with a full sized ATX motherboard. the reason for this is expandability. you may start out with a few hard drives and no video card, but then learn about the ease of use (and not to mention money savings) of running your own media server. sounds scary right? one youtube video will show you how crazy simple it can be. now youre thinking, “i want to do that, but i dont have a dedicated GPU.” what you do have is an open PCIe slot and access to abundantly cheap cards on ebay.
hard drives are also a very likely scenario. i started with an old SSD as a boot drive and an absolutely ancient 1TB western digital drive for file storage. i loved the setup but always worried about the mechanical drive failing on me and losing data. i went to 2 x 4TB seagate ironwolf drives to mitigate that risk. then i went the media server route and ran out of space. i expanded, then ran out again. eventually i ran out of SATA ports on my mobo and needed an expansion card (an HBA, but ill get to that in another post). now i need another PCIe slot. ATX to the rescue.
while doing all this, maintenance comes up. fans that get loud. the ever present need to blow out dust. swapping hard drives. adding cards. ad infinitum. the last thing you want to do is a full rebuild every time you want to do something small because the part you need to swap or the place you need to get to is buried under a bunch of other stuff because the case was engineered to be built once then left alone. servers need love. plan on putting in some maintenance for your server the same way you maintain your home or your car. you take care of your stuff and your stuff takes care of you.
the moral of this story (and the previous post – Tower or Rackmount?) is the best setup for ease-of-use is a regular desktop case with an ATX motherboard. parts are everywhere, cheap, easy to work on, new user friendly, and quiet enough to keep in the room with you. if this is your first foray into this world, stick with these suggestions and save yourself a lot of headache in the future.