I'm assuming that you have the knowledge required to make a motherboard selection based on the other hardware in the machine? I.e., compatible IDE devices, compatible expansion devices (no ISA devices), etc.?
Assuming that you know that, get whatever is cheapest. AMD tends to be cheaper, but if you are looking at older processors around 1 ghz, who knows what you'll find. By the way, what are the speeds you are looking to get?
Also, what kind of memory do the current machines have? If its not SDRAM, DDR Ram, or RDRAM, you will have to purchase new memory as well. I'm guessing that since they're older machines, they might have SDRAM.
If you need help finding processors, try a few sites. Probably the best electronics site on the internet is
www.newegg.com. The usually have close to the best prices, and they are extremely reliable. If you want to compare prices, go to
www.pricewatch.com. They collect price information from a lot of online vendors, and the website is usually a good measure as to the going price of electronics. Once you find a vendor with the price you are looking for, go to
www.ResellerRatings.com and look up the company by their URL (i.e. to find newegg's rating, look up
www.newegg.com). This way, you get the company you're looking for. When ordering from companies listed on pricewatch, ALWAYS look them up first on ResellerRatings.com. There are a few companies that advertise the lowest price and like to scam people...so watch out.
Anyway, to answer your question, the only way it matters is because it affects what motherboard you can purchase. I'm assuming that you want to find the best deal possible, so I would recommend that you compare prices. Depending on what you want to get, the prices will differ between an AMD system and an Intel system of the same speed, and it is very hard to tell which chip maker it will favor.