Usually I wear my old Montrail low top hiking shoes for bicycling. Sometimes lightweight, thin-soled deck shoes, which means I have to lower the saddle height just a bit to compensate for the difference in sole thickness. Good enough with my hybrid's wide flat platform pedals.
I switch between Nashbar baggy cycling shorts and a couple of pairs of cargo shorts I already had. The lighter weight cotton and poly or nylon blends are more comfortable in summer.
I tried to avoid getting too much into cycling apparel, but finally quit fighting things and got a couple of poly cycling jerseys. They're casual fit and style, not obviously bike-y. But the poly mesh fabric is much more comfortable than my cotton pullovers in summer.
And I tried a couple of different pairs of padded cycling shorts but found them unnecessary for my hybrid bike's padded saddle. And during the hottest, muggiest swampbutt part of the summer the padded shorts held too much perspiration and aggravated my heat rash. So last week I switched to
Champion tech fabric boxers. Very comfortable. The heat rash cleared up within a couple of days. Turns out I just didn't need the padded shorts with a padded saddle, and the Champion boxer undershorts are made with the same wicking fabric as most active wear shorts and shirts. And they support the boys at least as well as dedicated cycling shorts, so no problems with stuff getting in the way during longer rides.