is there such a thing as a rational color?

On "Rational color." Just because one has a strong emotional response to something, does not mean that thing in itself holds some identity that can be objectively related to human psyche. Consider the difference between having a strong emotional response to Hitler - and strong emotional response to the smell of your first girlfriend's perfume. In one case, there are objective standards, which can be applied to the object of Hitler. In the other, there is some personal association, which does not tell you anything about the smell itself.

There are German psychologists who claim that there is such an objective relation to human psyche, though. Something like, red implies health and vitality, yellow fantasy and so on. I am not inclined to buy such a theory without an overwhelming amount of statistical evidence. Even then, it is extremely unlikely that the basic objective relationship, should it exist, would not be overwhelmed by memories and associations for a particular person. Imagine growing up in the Soviet Union. Is your reaction to read about vitality or communism?

On "Canvas with two shades." No, it is not art, as you point out, by the definition of art, being "selective representation of reality." However, not everything pretty must be art! How about decoration? Nice paint job? Screen saver? Wall paper? We pick all such things amongst concretes that make us feel good without making the claim to art.

On "Loving a green canvas." It is rarely bad to love anything, unless there is specific evidence of depravity required to love something so obvious appalling (again, think: Hitler.) Wind chimes, colored canvas, a plastic bag dancing in the wind on the pavement, the smell of coffee, the sound of a child breathing... A thing doesn't need to be art in order to be loved.

On the main question concerning preference for a particular color, I agree with Kate that it's primarily a matter of individual context. Philosophically, I would add that it also pertains to the issue of "optional values," which is recognized and upheld by Objectivism.

From the question:

[W]hat does it mean to have a strong emotional response to things like pure color? Ayn Rand herself famously loved blue-green and it is clear it made her happy to see that color.

Given that she had this well documented emotional preference for the color, does it follow that this feeling is "rational" and that some colors are "rational" while others are "irrational" ?

No, "color as irrational" does not follow, because the values involved here are optional. Two or more values can be equally rational, depending on an individual's own context. (This doesn't mean all values are optional, of course.) One reference regarding optional values is OPAR, pp. 323-324 (end of Chapter 8).

There is another subtlety in the question:

...(according to objectivism) all emotions and reason are happily intertwined and in some ways the same....

Remember the difference between "are" and "can be and ought to be," which do not have the same meaning. All manner of emotional problems can arise if one defaults on the use of one's rational faculty, and rationality (reason) is always volitional.

More broadly, life is mostly about options and choices (and freedom to pursue them), not rigid "commandments." In the words of John Galt [FNI pp. 142-143pb]:

If I were to speak your kind of language, I would say that man's only moral commandment is: Thou shalt think. But a 'moral commandment' is a contradiction in terms. The moral is the chosen, not the forced; the understood, not the obeyed. The moral is the rational, and reason accepts no commandments.

My morality, the morality of reason, is contained in a single axiom: existence exists—and in a single choice: to live. The rest proceeds from these. To live, man must hold three things as the supreme and ruling values of his life: Reason—Purpose—Self-esteem. Reason, as his only tool of knowledge—Purpose, as his choice [pursuit] of the happiness which that tool must proceed to achieve—Self-esteem, as his inviolate certainty that his mind is competent to think and his person is worthy of happiness, which means: is worthy of living. These three values imply and require all of man's virtues, and all his virtues pertain to the relation of existence and consciousness: rationality, independence, integrity, honesty, justice, productiveness, pride.

This is followed in GS by an entire paragraph on each of the seven virtues.

Objectivism is also concerned with greatness. One reference appears in VOS, Chap. 11, p. 104pb:

Greatness is achieved by the productive effort of a man's mind in the pursuit of clearly defined, rational goals.

And again, from Ayn Rand's "Introduction to the 25th Anniversary Edition of The Fountainhead":

It does not matter that only a few in each generation will grasp and achieve the full reality of man's proper stature—and that the rest will betry it. It is those few that move the world and give life its meaning—and it is those few that I have always sought to address. The rest are no concern of mine [they are neither great nor evil]; it is not me or The Fountainhead that they will betray: it is their own souls.

Unlike so many religions, Objectivist morality does not attempt to intrude into people's lives and declare them to be moral or immoral in everything they do, nor to prescribe and rule every detail of their lives. Objectivist morality is concerned, above all else, with identifying what human greatness is and how to achieve it, and with upholding and defending it from all manner of attempts to undermine or destroy it. It is the destroyers (man-haters) who receive Objectivism's most intense moral wrath. Those who are merely neutral and respectful are viewed respectfully and neutrally in return. And authentic, persevering man-worshippers receive Objectivism's highest moral praise and admiration as the heroic beings that they are.

There is a vast spectrum between greatness and evil, a spectrum of less-than-great yet far better than evil, a range of fundamental decency in the pursuit of happiness on as modest or great a scale as one chooses. Except in America, there is little else to say about that intermediate spectrum, other than to recognize what is possible to man and on what terms.

Ayn Rand regarded Americans in general as exceptional. Refer especially to her two-part article titled, "Don't Let It Go," republished in her book, Philosophy: Who Needs It. Here are a few representative excerpts:

Americans are the most reality-oriented people on earth. Their outstanding charactreristic is the childhood form of reasoning: common sense. It is their only protection....

Americans are anti-intellectual (with good grounds, in view of current specimens [December 1971]), yet they have a profound respect for knowledge and education (which is being shaken now). They are self-confident, trusting, generous, enormously benevolent and innocent....

Defiance, not obedience, is the American's answer to overbearing authority.

This article also contrasts Americans with Europeans while describing the downward trends in America, and offers a sobering prescription:

[C]ommon sense is not enough where theoretical knowledge is required: it can make simple, concrete-bound connections -- it cannot integrate complex issues, or deal with wide abstractions, or forecast the future....

[T]he American view of man has not been expressed or upheld in philosophical terms (not since the time of our first Founding Father, Aristotle; see his description of the "magnanimous man").

I hope all of this helps to make more concretely real the nature of Objectivism's perspective on man's life, the role of morality, and conditions in the world today -- all of which I see implicitly in various aspects of the question as formulated (like the tip of an iceberg capable of sinking a Titanic).