My bike commuting clothes are really totally different from my going-on-a-bike-ride clothes. Bike commuting clothes are just my regular clothes, since I bike everywhere.
They're not bike specific, but I swear by black BDU (army) pants, which I order online. They have nice big cargo pockets, and the seat and knee are reinforced. They have a few fabric options to choose from. I like the 100% cotton best, but the cotton/poly twill is also very comfy, dries a little faster, and is very colorfast. The size I get is roomy enough in the thigh to ride in comfortably. Actually, my better half is the same size so we just share. We have a whole pile of identical black pants, and if they start getting holes (which takes awhile, they last a long time) we just get more of the same.
I wear cotton flannel button-down shirts, often with a wool or fleece vest or sweater, and a waterproof/breathable jacket that I made. I wear Chippewa water-resistant insulated work boots all winter.
And I'm always trolling sales looking for good undershirts. I just can't bring myself to pay that much for an undershirt, even though I know they're probably worth it.