Wow, what a loaded question!
To get started, take a look at this old but useful explanation of
High Performance Networking Unleashed - check out Part 1, Part 4, and Part 5 for starters. Although it looks at UNIX, NT4, and Netware, as a possible OS to choose, it will give you more info on the other things you need to look at.
Realize you are asking "What do I use?" You aren't giving enough information (and probably can't with all the variables involved). It is like asking "I love to travel, what mode of transportation should I use?" You could get opinions about any one of the following as being perfect for traveling: bicycles, boats, planes, trains, automobile, or feet. But since you don't give enough information, some of the answers may not work. If you don't mention you live on an island in the middle of the Pacific, and you want to travel around the world, then a bicycle would be useless - unless of course you can hold your breath for long periods. If you don't mention you are afraid of flying, answers of planes would be useless and a waste of your and our time.
I hate to even ask some of these questions, and don't think even if you answer them here that anyone could give you the correct information. It's something you have to get through with the company you are working for.
1. What are we trying to accomplish? Is this server to be used for web hosting, financial reports, accounting, mail server, (and the list goes on....)? Will the software running the application run on UNIX/Linux - and if so, which ones? The software itself may give you a list of OS and versions that it works on cutting down on the list that you should look at.
2. What type of support is the company looking for? Is this a 24 hour, 7 day a week server (they usually are no matter what, but when it comes down to it, what is the company willing to spend on 24X7 - normally they start by saying they want 24X7 but they usually end up not wanting to pay for it - fault tolerant, clusters, disaster recovery, backup...) How much money are they looking to spend?
3. With the lack of knowledge of UNIX at your company, why are you attempting to use it and build a server that no one knows how to support? How was that decision reached? And can we fire that idiot?
As far as your original questions:
1. Motherboard and processor: any special requirements?
This will matter on the UNIX OS you decide to use. Most sites that offer either free downloads of Linux/UNIX will have a hardware compatiblity list. Once you have a better understanding of your needs as far as the business requirements, you will have a better understanding of which possible versions of OS will fit your needs and can then cut down on the large list of possible hardware that will work.
2. I'm buiding a UNIX server box. With all the flavors of UNIX I'm really confused as to which one to buy/download. I'm a newbie but it is quite important that I learn a flavor that would help me the most no matter what type of UNIX box I come across.
Since most UNIX/Linux is based on either (or both) BSD and System IV UNIX, you will find most are compareable but each has it's own quirks and going from on to the other is usually a pain. Just as each programming language uses the same logic to get something done, each uses different syntax in it's language. Being a newbie, don't worry about what would help you the most no matter what box you come across. You only have two months - you will have enough problems with getting all this working. Once you figure out the answers to some of the questions and have a better understanding of what OS you may be looking to go towards, you can either look for a book or on-line tutorial that will help you get a feel for the OS and assist you in that learning curve.
Check out the FAQ s listed below.
3. Where could I get this OS at?
If your looking for free software, a quick search on the web will give you many choices - check out the FAQ section of this site for more info on different places to download different sites
FAQ on this site