For me, it's what's the best overall price-performance I can get. I commute on some Michelin Dynamic Sport slicks at 700x28. Good balance of comfort and performance. And knock on wood, no gowges, no flats in 700 miles or so. (Just wait, I probably cursed myself and will get a flat riding home tonight...). But I also commute on 700x32 tires. Really comfy, and both I can get tires for around $14 each.

However, in the rain, I ride my drop bar mtb commuter with bar cons and fenders. Those run 26x1.5 inverted tread tires. Very comfortable and they corner and grip great with their narrow tire profile mounted to Araya RM20s or Sun Rhyno-lites. I think they're IRC Metro IIs or something like that. Great value as well at just $12.50 ea when I bought them a while ago.

So the wheel size really depends on what tire size is on sale and good for commuting.