Q:

Why did the clones' blaster color change?

In Star Wars Episode II: Attack of the Clones and Episode III: Revenge of the Sith the Clone Troopers mainly use blasters that fire blue:

However, in the Galactic Civil War era the troopers mainly use blasters that fire red:

Why is that?

A:

The explanation with good evil is ... well ok-ish I guess. BUT
The Clone troopers used the DC 15A blaster rifle for most of their active time. It was the standard issue rifle.
The Storm troopers used E11 blaster rifle. The E11 is based on the DC 15A and it had 3 settings (lethal, stun, sting). The E11 was standard issue for Storm troopers.
So beam colour can be because it was an ENTIRELY different weapon or it can be because clone troopers used stun and sting settings and Storm troopers only used lethal setting. (speculation on my part here)

A:

The switch from red to blue signified the clones fall from grace. Throughout the SW films, blue represented good while red represented evil.  

A:

In the EU, the gas used in the blasters indicated color. 
Speculation:
The Republic may simply have used a different provider before becoming the Empire and color changed as stocks of the blue gas dropped. Also, different versions of weapons, such as cannons verses hand weapons, might require a more condensed gas or a different type of gas to maintain the excited charge.
As the Republic became the Empire and mopped up the Separatists, they would have more access to the production of other gasses, and over time those gasses may have been easier to produce or Imperials (and Palpatine) changed the color to signify a new order in the galaxy. (Not the NEW ORDER of Episode VII, but a new government.)

