Thank you everyone for taking the time to explain this - and for generating some animations.
I am pretty sure that I understand why the clocks appear to run slow from the perspective of an observer (the final animation was very useful as I had not grasped why the stationary clock would also appear to run slow). To avoid a convoluted reply, I will not quote people directly, but one of my confusions was why does time pass slower as you move faster. I wonder if either: I have missed this part of understanding from the replies (Mordred, your reply may have covered this, but alas, my knowledge is not good enough to follow everything with clarify). Or the light clock example does not cover this particular phenomenon. But first, some follow-up questions on the light clock specifically:
1) Isn't the light bouncing back and forth (not at an angle) only an illusion for both observers? Even if you set the clock on a table on Earth, the Earth is moving and rotating, so the path the light takes is not directly up and down - even though it appears to. If both the observer on Earth and on the spaceship were to take a map of the night sky and plot the path of the light of the clock in the spaceship (as in the above animations) based on where the ship was each time it hit the mirror - would they plot each 'tick' at the same point in the sky? Maybe this is a pointless question, but I feel that what is actually physically happening is that the light is bouncing at an angle for the observer in the spaceship, they just don't see it.
To approach it from another angle - there is a certain amount of 'physical action' occurring. The light does physically bounce at an angle, independent of who observers it and from where. Is that right? Does that not play into the scenario at all? Or is that cancelled out in the scenario?
2) This is a stupid question, but, how does the light bounce diagonally? If the light hits the mirror dead on, it will bounce back on the same path and miss the top of the clock, which has now moved. Or is the light purely metaphorical in this example? I know it's not relevant to relativity at all, it's just bugging me.
3) I fully get the each clock will appear slow from the perspective of the other observer. But that now throws a big question for me. Let's assume that the stationary clock has absolutely no velocity at all (not even planetary rotation). In a crude way, we can consider this recording 'true' time, as there will be no relativity effects from it's own movement. Apologies if this analogy butchers all known science, I just find it useful to use a concrete frame of reference. In any case, our moving clock will appear to tick slower from an observer at our stationary clock and vice versa. You then bring the clocks back together and the moving clock shows less time to have elapsed. So is the stationary clock appearing to run slower for the observer on the ship purely an illusion? Time does run slower for the observer on the moving ship, but time is evidently not running slower for the observer at the stationary clock - it just appears that way due to the behaviour of the light. Would the moving observer see their clock at 22:00, look at the stationary clock and think it says 17:00, then put them together and see that the stationary clock is in fact reading 05:00? Or have I completely missed this point?
OK, on to my remaining point of confusion. Janus ended their post by saying that this behaviour does not affect time. I presume they mean, the classical point, that if you travel really fast, you age slower. Do you just mean that the light clock analogy does not explain this behaviour? Or that moving fast does not make 'time slow down'?
To go back to my original analogy:
4) If you have two perfect mechanical machines that make a mark on paper every 10 seconds (defined by the workings of the machine, not by a measurement of 'time'). One machine with each clock. If you stopped both clocks and both machines when the stationary clock reach 60 seconds, which of these is true?
a) Stationary clock reads 60, stationary machine has 6 marks, moving clock reads 30 (for example) and moving machine has 3 marks
b) Stationary clock reads 60, stationary machine has 6 marks, moving clock reads 30 (for example) and moving machine has 6 marks
The essence of my question is - regardless of how fast you are going, can do you do the same amount of physical stuff? The 'faster you go, slower you age' idea suggests that you do less stuff and the machine would have 3 marks. If that is the case - can someone explain why? How can the speed you go physically alter the amount of physical effort that be completed? I'm guessing there is an additional component needed to explain this.
5) After having just watched Interstellar and being to a Brian Cox talk, I feel I have a good beginner understanding of black holes. Brian's use of the light cones actually, for the first time ever, showed me exactly why light can't pass out of the event horizon. So, there is time dilation caused by a black hole - but the additional explanation given here is gravity, which 'bends/pulls/stretches' space/light/time - thus making the distance to be covered larger than can be covered in the time - or something to that effect. My question is, how does the gravitational effect match onto the light clock? Is it the same effect and that gravity also lies underneath the light clock explanation? Is it the same principle, just applied differently? Or is it two different ways of getting to relativity? Again, I feel like I'm on the wrong track here.
Final, unrelated question, but this bugged me when Brian Cox explained it. The universe being flat - very briefly, I completely followed the principle that if you measure 3 points, you get a triangle and if the angles add up to 180, then it's flat. Less than 180 and it's saddle shaped, more than 180 and it's more spherical. I also get the caveat that the slice of space we're looking at is so tiny, it just looks flat.
To preface the question - I have no real understanding on the geometry of space, so I'm probably visualising this all wrong, however...
6) The universe is obviously 3D and we pick 3 points in space to do our triangle. But if you are inside a square, rectangle, pyramid, saddle, sphere or whatever and you don't know where the sides are and therefore any points you pick are inside the shape and not on the surface then surely it's all flat, whatever way you slice it? 99.99% of the slices you can take out of a sphere will be flat - it's only if you include 2 points on it's surface that you will get a curve? My guess is that it's not just the idea of the shape of the universe being flat, but that actual construction of the universe. Are we saying that in a saddle shape universe that what appears to be a straight line is in fact concave? If you bore a straight line through an apple, that line is straight, even those the surface is not - would that same bore hole be curved in a non-flat universe?
Maybe I should have studied more Physics at school...