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:
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)
In the EU, the gas used in the blasters indicated color.
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.)
My answer: An in - universe explanation is that the blaster colour was determined by gas color, and the Republic and Empire had access to the high quality green and blue gas. The Republic may have also used ion bolts (which are blue) to counter the Separatist battle droids. When the Empire took over, the Stormtroopers began using a new type of blaster, and Palpatine may have chosen red as the color of their blast to show change and terror. The Rebels most likely used all red bolts because they were cheaper. An out of universe explanation would be that in the originals, the colours weren't well planned, so everybody used red blasters and the Empire used green turbolasers to look terrifying in evil. While in the prequels, more had been planned and they had more money, so the clones stuck to mostly blue to symbolize good, and the Separatists used all red to symbolize evil
Technically, I believe, the clone troopers also used blasters with ion charges that are more effective against droids (ion weapons surpass armor and affect computer/machine systems). As the clone wars wind down into a resistance against terrorists and dissidents of a biological origin, then the expense for ion charged blast bolts is not needed by empire troops.
Its just used to distinguish good from evil for the viewers. For example, in SW: The Clone Wars S05E01, some of Hondo's own men turn against him, and their blaster shot colour changes from blue to red while Hondo's other mens blaster stay blue. Now, everyone in the same team usually has the same blaster colour, right? And they coudn't have changed their colour to red just because now they're the "bad guys." To themselves, they weren't bad. So the colours are just to show to the viewers that blue is good and red is bad from the point of view of the main character...
I think it depends on what rounds they used. The clones had rounds that shot blue. It could have been to signify their side. But maybe the rounds were tested and it just so happened that the most efficient rounds were blue. If you watch Star Wars the Clone Wars or play Star Wars Battlefront 2, then you know each gun can shoot any color. For example, on several occasions especially with the pirates, they had DC-15a blasters or sometimes ever DC-17 pistol. But they were shooting a different color besides blue. The pirates shot red rounds out of them, and I think someone else shot green. In Battlefront 2 when you change the type of ammunition for the DC-15LE and several other guns, they shoot a different color. Red, blue, or green.
Ok, these are all good theories. Practically speaking, Georgie wasn't planning ahead with all the more after the first movie. Red is there most easily recognizable "laser" color. Green lasers are quite common as well. It's recognizable. In the originals, there was somewhat of a difference made between space and the insides of ships, surface of planets in terms of lighting. Most blasters were red. Spaceships shot green stuff because it was. Sickly looking, and gave the right atmosphere. Blue was part of the image overhaul that changed fiercesome Stormtroopers into 'heroic' clones...
The reason why clone trooper blaster bolts are blue is because the bolts are actually plasma. Plasma color was blue. Red color I a'int really sure what it is. Green blaster bolts I a'int sure either. The only time we see green color bolts is in The Phantom Menace when Padme and some other troops capture Nute Gunray. If you want to count the genosian guns as green bolts (even thought they are green color) you can. Hope this answers all questions and helps.