Perhaps I'm just not smart enough to design that kind of thing, but I think a lot of it happens sort of naturally. About the only thing I consciously do, all other things being equal, is to make sure some greens have a bit more or less slope overall than the "typical" green on the course. I hope (have never actually field verified this) that golfers can't get a read on how greens are breaking that day, as in, "the last putt broke further than I thought, so I'll aim outside a bit more."
Besides grain, a green on hilly ground can sometimes mess with break reads. I once remodeled a green that didn't drain, and when surveying it, I found it was actually just flat because it was at the base of a mountain, the shaper did it by eye, and thought it was tipping away from the mountain, but it wasn't.
I actually tried, just that once (wait, I did it once in Colorado, too) to tilt the green to the mountain, and it just looked weird. Most people know (I think) that retaining walls are actually built slightly back into the slope because if they were built truly vertically, they would look like they were tipping out.
Most golfers know that greens break to the water because it's the easiest most natural way to get water where it wants to go. But, with digital levels, they find out that it really breaks more than the USGA recommended 2-3%, usually by necessity. If you are building a green on a 15% cross slope, fitting it in close to level also makes it look like it's tipping back into the hill, and it can be very difficult to fit it in. Sometimes, raising that cross slope to 4-5% is required, which of course was much easier back in the day of slower greens.
I mean, physics is physics. A ball will break downhill, more with greater green speed and sharper slopes, and less when hit at more velocity. For some reason, putts that trickle away from you seem to break more than others (i.e., break to the right, especially downhill for the right handed golfer, vs a break to the left). The reason some putts appear to break further than golfers think has to lie in the outside environment. If a gca really wanted to mess with perception, he might specify that all trees near a green be planted something othe than vertical, all leaning the same direction, LOL.
Of course, this includes the well known tendency of golfers to under read breaks anyway.
I will be interested to hear what other gca's have to say.