Toxicity is indeed a great album, but I can't stand Chop Suey! with or without its current meme status. I can see the appeal in the choruses but the verses are just... too annoying and impossible to take seriously. While I certainly wouldn't say SOAD is an underrated band, part of me feels like they'd be even more respected if that wasn't the song people immediately thought of when they're mentioned. B.Y.O.B. is much better as far as their "hits" are concerned, imo.
As far as my favorites from Toxicity are concerned, I'd probably go with Needles, Deer Dance, and Aerials.
I like B.Y.O.B, but I'd surely take Chop Suey! over it...You might be right, though, about the "general" public's perception...There is so much more than the "nu metal" tag that was assigned to them (especially after Toxicity).
Great picks for the favorites, btw...Those are mine too, although I'd add, well, Chop Suey!
and Science (its chorus' melody, in a VERY weird way, reminds me of Rush's The Body Electric). The title-track (overplayed as it may be) is great too.