Question #1 AMD or Intel : Both processors do the same thing and are compatible with the same programs. AMD is less expensive in general and has very good performance. I have AMD processors in both my Laptop and Desktop. Currently Intel has the fastest processor, the Core 2 Duo. If you have the money to get a machine that has a Core 2 Duo, go Intel. If you are looking for something less expensive, go AMD.
Question #2 Windows, Apple or Linux: If you are a tech savvy person and compatibility is important to you, I would say go with Windows. Windows can be a pain when things get messed up and is EXTREMELY open to Viruses and Spyware, but there is more software out there for Windows than any other OS. (Be Warned; A new version of Windows is due out in January. If would be worth waiting so you do not have to upgrade, and it's kick a$$!!!)
If you just want a computer that works, out of the box, go with Apple. They are more expensive, but are gorgeous machines. OSX is not natively compatible with Windows Programs, so you're not going to be able to walk into best buy and have a huge selection of software to choose from. That said, Apple includes basically everything you need out of the box. This also makes Apple a better value, because you don't need to buy more software. It comes with Tons of Software, including Apple's ILife Suite for creating Digital Media, etc. THERE ARE HARDLY ANY GAMES FOR OSX. This is the reason that I don't have an Apple. Apple is working on that and an advanced user could install Windows on a Mac and play games, etc.
Linux is FREE! Ubuntu is the most popular and easy to use Distrobution (They are in general all based on the same core). You can install it along side Windows or Mac OSX. There are distros out there for AMD, INTEL or PowerPC. If you are not an advanced user, I would not suggest going the Linux route. Sounds great, but installation can be painful and although once you have the OS installed, you are using a full GUI, similar to OSX or Windows, you will often find yourself typing in commands into a shell. Linux is a good OS, but I would suggest getting a OSX or Windows machine and then mess around with installing Linux along side one of the other OS'es or just playing around with a Live CD.