Reference Designs for Analogue & Digital Inputs to Microcontroller
This is a very general question and there are lots of app notes with reference designs for mixed signal boards. "mixed signal", "digital analog", "design" and "ground" are your keywords. In addition, usually every datasheet of a mixed signal controller or DAC contains a reference design.

A common method for protecting analog inputs is a Z-Diode and a series resistor. You have to realize the overvoltage protection requirements and the DAC leakage current to calculate the series resistor value.
As you can see in http://www.atmel.com/dyn/resources/prod_documents/doc2508.pdf a series resistor can protect an analog input even from mains voltage.

Yes, you can use a resistor divider for scaling an analog input. If the input resistance is too low, use an transistor/opamp as a voltage follower.

For digital inputs you can use resistor dividers/series resistors, too, which is the slowest of the mentioned methosd. For up to 15V you can use a 74HC4050 buffer. If it need to be really quick, you're probably better off with a dedicated level shifter IC.