I suspect the number of potential good commenters who were discouraged by participation by mass-downvoting after having posted their first five or ten comments might exceed all the other damage done by Eugine. (I don't have the relevant data, though, only anecdotal evidence.) Please note that this is Eugine's explicitly stated goal.

The moderators' time wasted is not so big in absolute numbers, but LW is quite self-moderated, so there is only minimum action that needs to be done directly by the mods. However, from that small amount of direct action, I would guess that maybe a half is Eugine-related (maybe except the recent "LessWrong 2.0" planned changes). It can be quite frustrating to become a part-time Eugine's babysitter.