I laughed a bit when I first read this question - I'm not sure you understand its scope. One could literally write a book about this album and its meanings.
First of all, you absolutely must not take this lyric (or its song) out of context as you interpret the album.
This album, like most art (and the moon), revolves around many concepts and ideas. Interpretations may vary. There are many, and ALL of them are potentially correct. A work of art like the Dark Side DOES NOT have a single 'point.' Its meanings are numerous and subjective. However, here is the one I prefer:
At the beginning of the album, we hear the lyrics
All you touch and all you see
Is all your life will ever be
Run, rabbit, run
Dig that hole, forget the sun
When at last, your work is done
Don't sit down, it's time to dig another one
The above is a major message constantly regurgitated to us by society. Work, work, work, work, work. Just work for the good of the whole. Your life consists only of your perceptions and actions, and it has no special meaning whatsoever.
This sets the stage for a statement about the nature of the human society in which we live.
In Time / Breathe (Reprise), they further reiterate this dull, clocklike, mechanical existence. When the lyrics 'Home, home again' appear, the subject is essentially taking a break from reality for a moment returning to the dwelling of his personal thoughts and internal existence. Presumably, this break continues throughout The Great Gig in the Sky, after which further statements about the superficial and sometimes hostile nature of society are made in Money and Us and Them.
Any Colour You Like is harmonically related to Breathe and its Reprise - this implies that another break from society / reality is being taken.
When we come to the final moments of the album, the clocklike existence of the exposition is about to come to an end. It is difficult to put this into words, but I will try. The idea is not to over-interpret every word here, but to get a general idea for what they might be saying.
And if the cloud bursts, thunder in your ear
You shout, and no one seems to hear
Here you've clearly perceived something that was loud or monstrous in nature (note that the cloud is REAL and concrete - not an insane musing), you are shouting about it, and no one SEEMS to hear you. Do they actually hear you? Perhaps they do, but they are too caught up in their monotonous existence to acknowledge your shouting. This may also imply a certain apathy by the people (society) to whom you are shouting.
And if the band you're in starts playing different tunes
I'll see you on the dark side of the moon
The first part of this is an idiom, commonly used in a few different variations:
He plays to a different tune.
He marches to the beat of a different drum.
This implies that, though the subject may or may not be insane, his perception of reality and / or behavior is decidedly different from that of the rest of society. "The band you're in" may imply that this unique behavior / view of reality can apply to a group or collective at times as well as to the individual, or it may be in reference to multiple aspects of self. So if you march to the beat of a different drum,
I'll see you on the dark side of the moon.
The dark side of the moon is the same idea as was presented in the lines about shouting about something you've seen, and no-one seeming to hear you. Society either cannot see what you are seeing (in the same way that we cannot see the dark side of the moon), or they are so caught up in their lame, clockwork existence that they are unwilling to acknowledge you.
This has so many implications - spiritual, religious, societal, psychological. It works on many levels.
And at the very end of the album, we are assured that no matter what we perceive or do, be it right or wrong - sane or insane - that everything is working in tune. The clockwork, apathetic, monotonous existence of society, the moon, the Earth, and indeed everything in existence - both concrete and abstract, seen and unseen - all work together to create and sustain the reality in which we live.
It is both a lamentation and a warning.
But it is also a message of hope.