I use the caps that came with the bottles. (I'm talking about twistoff caps for plastic soda bottles) I think you can also buy new caps at bigger LHBS's, or mail order. I don't reuse metal crown caps.
I should probably go thru my glass bottles and get rid of some -- probably keep the longnecks, stubbies, and anything bigger than 12 oz, and get rid of the mid-sized bottles like Sierra Nevada (they don't fit well in a milk crate) Or else build some kind of stackable crates to hold the SN bottles.
"Talk very fast, hope something good happens, take the credit" --The Doctor