When I was out in SF for MacWorld, I made a little side trip out to Cupertino so that I could see the Apple campus and of course buy stuff at the Company Store. Fun! Got some t-shirts and other things with the Apple logo. I was ecstatic to find that they had some items in orange, which is my favorite color, so now my Mighty Mouse is sitting on an orange mousepad with the white Apple logo. Love it!
They were nearly out of stock on the "I visited the Mothership" shirts, so the one I got is huuuuge -- better suited as a nightshirt for me than as a shirt for wearing around town, but that's OK.
Yes, you can buy vintage Apple clothing and other items online through places like the Missing Byte. I've gotten a few things from them.