There are probably plenty of bands with lyrics so complex you wouldn't understand the meaning of any of it. I don't consider that a good thing.
If you want intelligent lyrics, however... Not too sure. Occasionally Dream Theater, I guess. One of my favourite lyricists is Devin Townsend, but a lot of his stuff appears to be gibberish, it's just gibberish I'm very fond of. I also like early Machinae Supremacy lyrics, but I dunno about complexity and such, it's just well written punk lyrics, mostly.
And I second At the Gates.
(I know I probably forgot about some lyrically awesome band)