Do numbers in skills scale or otherwise change?

The truth about these numbers is much more mundane. Simply put, the way the abilities are coded, all of the green numbers are variables.

For Runes

Runes used to have quality levels, with each successive level of rune increasing the efficacy of the skill. This is why runes like Arcane Torrent's Cascade list "a 100% chance", instead of saying "whenever" or "always" -- if you used a lower level rune, it wouldn't be a 100% chance.

For Abilities and Passives

For abilities, the thinking is mostly the same, though the rationale is different. Essentially, by designing the abilities in the way that they did, they've made it very easy to tweak and balance the individual abilities against each other.

Consider, if you will, Bolas Shot.

Notice which values are in green: The hatred generaiton, the delay, the initial damage, the splash damage, and the splash range. Now imagine that Blizzard determines bolas shot to be horribly, horribly overpowered. They have to nerf it. What do they change? Well, because of the way they built the game, they already have 5 "knobs" to tweak in an attempt to better balance it - the five variables in green. Even when one of the green values isn't affected by any of the five runes, it's still useful as a tuning mechanism.

This happened in beta all the time - the balancing patch notes would always tweak the green values, and leave the rest of the ability untouched.

There is also a subclass of skills and abilities which have the green text because they scale with level.

Most healing abilities are this way. In these cases, the text is green to signify that the value is not constant (because, again, everything in green is a variable), and is used instead of listing a formula (which would be constant, but would be bothersome to calculate manually each time it changed).

Even here, the underlying formula can be changed, with the same results as tweaking the formula in one of the non-scaling abilities above.

Color of numbers:

As you said the green color is used to make them stand out, you mostly remember what your skill does but there are many occasion you want to recheck some of the values, one of them often being skill damage comparison.

Due to mixed types of values we can't say that green is used to mark values that change which is usually the case.

Value of numbers:

• Some of the values change by using runestones,but note that some skills completely change the way they work,so adding runestones actually changes the text along with the numbers.

• Some values are constant during the whole game like some cooldowns,stun duration,mana costs,number of hits...

• In D3 many skills use weapon damage percentage instead of actual skill damage to balance the game between melee and magic classes as they gather better and better equipment and progress levels.Because of the use of percentage on most skills there is not so many scalar values.

• Some particular values are not in percentage and they have to scale with the player level to keep their usefulness on higher levels.Transcendence(monk) is one of those skills.Most likely these values are not in percentage to prevent their abuse and make them balanced in certain parts of the game depending on what point the blizzard thinks someone to be unbalanced...i still think they could be replaced by percentage in future.

The green lettering indicates aspects of the skill that can be modified by runestones. If you look at the runestone tooltip after you apply the runestone you can see how it affects the skill. For example when "Clobber" is applied to "Bash" you can see the 20% chance of Knockback is replaced with 35% chance to Stun.

There is an awesome calculator here where you can see different effects.

Since it's just a number value, it is used to make it stand out more so that with quick glance you know what you are looking for. You see the green and know it's for a #'s value. A quick glance is all you have time for as opening your skill bar does not pause the game.