Do specials or OVAs count? Zero no Tsukaima's (season3?) OVA is easily the worst animation of any variety that I've ever had the misfortune of needing to watch. Needing, because I can't not watch any and everything related to whatever series I'm going through. As if that series wasn't bad enough.
But if specials/OVAs don't count, then the two lowest scores I have on my MAL are Otoboku and Children of the Whales. Otoboku was probably the worst of the two, but I think I like Whales less simply because it could have actually been decent...if only it had ever done anything at all.