In my opinion Linux OS is a best choice for newbies to learn embedded system. As It is an open source system,which could help learners gradually master this embedded operation system through many times researches and tests. At the same time, it also is a successful software platform that has been widely applied in many fields.
What about you?
If you mean which OS I'd use for microcontroller programming I'd say linux. I've no problems of any kind with ports and drivers and it is all under your direct controll. This is good if you have enough patience to learn how to manage the power the linux's tools will give you. Don't know about windows, never used it for development, but I'd say avoid mac os. I'm working with some collegues who love the apple line-up, and on their computers we are having some troubles, especially with serial communication to the boards. Also, I think that Linux is widely used in the fild so in case you need support you're likely to found it pretty easily. Best regards, Andrea