Ooh, ooh, I have an idea (and I'm actually being serious here)! Why not arrange those units in order of disappearance, as it were, starting with all the Vanilla units who have no equivalents in EB, moving on to units dropped after 0.7, then the old Sweboz units or the Roman units before they were reskinned or whatever - just arrange them chronologically.
Incidentally, having them all in a box of somekind in the middle of the page with a horizontal scroll bar should give the impression of walking along a museum corridor. Each 'display' could have the unit's picture with a brief description of what the unit is and why it was scrapped at some point (or, in the case of the Vanilla units, never included) underneath.
Er ... unless you guys want to hide all traces of old units, that is.