Didn't Iron Giant come out at a time when animation studios got onto this kick about cranking out "adult" animated movies? I remember when The Road to El Dorado came out, everybody was like, "Parents, be advised when taking your kids to see it, there's some bad language in the movie", etc (y'know, back when grown-ups still cared about the kind of language their kids used, as opposed to today when they think it's acceptable for kids to swear once they get out of kindergarten). And wasn't that Disney movie Atlantis supposed to be rather "adult" as well? I think perhaps Iron Giant can be forgiven for that...
Incredibles aside (yes I'm aware it was toned down a bit from Bird's original concept), I think any innuendos in Ratatouille are rather subtle and are mostly played for laughs; the biggest one would be Linguini himself, considering he's basically the illegitimate son of Gusteau, since he was born out of wedlock, but other than that, stuff like one of the chef's being fired from the circus for "messing around with the ringmaster's daughter", and brief awkwardness after Linguini finally admits his feelings for Colette (yeah, I know there's a brief moment where the shot is supposed to be through his eyes, and he's checking out her butt for a second), those are subtle and played for laughs.