Welp, looks like clear pipes grow algae, but after the initial scrape off seems to grow more slowly.

I have two solutions.

One is rather obvious, its a pipe cleaner -- a wide one. The vertical placement of the clear pipes allow me to have open ends on the tops. Stick the pipe cleaner in there once every three weeks or so and they stay visually nice.

The second method is for my downward flow. I filled the bottom four or five inches of the down pipe with marbles. This creates enough back pressure to 'tumble' the water around and seems to greatly reduce the algae growth. Air bubbles often get caught in the currents, an in my possibly overactive imagination helps to oxygenate/aerate the water.

I think my clear pipe adventure is complete now, having understood why, why not, and what is involved if you still want to.

Thanks for your replies.