I *think* that the colors of the rune on the stone is tied to whether or not you can summon from it. But I haven't tested it. By this logic, green and red = "You are not in the correct level range for this stone" and Orange and yellow let you summon.
Similarly, when you mouse over a stone, the tooltip shows up in the color of a mob; Red, orange, yellow, green or grey. Orange, yellow and green you can summon from, or be summoned to.
/speculation

I thought I remember seeing a blue one somewhere in Northrend. Blue doesn't really fit in that scheme. I don't think the color changes. I think they just choose a color that fits the environment like red in Blackrock Mountain, blue in Northrend.

I just tested this on the Stockades... the stone had a yellow glyph to my 27 Drae Warrrior and my 80 Drae Shaman, so it doesn't look like the colors relate to your levels.

Its aesthetics, primarily (though probably not 100% of the time) the glow matches the lighting and dominant landscape colour around it, if your a grassy area with trees then the glows green, in a red barren area then red, in a dark creepy area then blue, etc...

I always thought the difference in colors was how they showed you what kind of stone it was, as in was it a 5 man stone (with level restrictions appropriate to the area it's for) or if it was a raid stone (like karazhan).

I wonder if it ties colour to classes... probably not.