If you are going to do an engine swap it doesnt matter which model you get.
Pretty much any B-Series, K-Series, H-Series engine will fit into a 2000 Civic, its just a matter of how much you want to spend on getting it mounted with the proper transmission.
If it were up to me, I would go with a B16C5. But then again B16C5's are hard to find, and therefore expensive.
If B16C5 cant be found, you can never go wrong with a K20A swap.