I really think if the toy is relatively simple and open-ended it is probably fine. DS (nearly four years old) has mostly wooden cars/trucks/tractors but he has got a few plastic and metal ones as well.
Plan toys makes some great wooden construction vehicles which are small (around the hot wheel size) and fairly detailed which most boys seem to like.
We have never done TV or characters with DS so he has no idea what or who super heroes are- but he does have that "hero" side to him and appreciates toughness and bravery. He loves knights, specifically Saint George. He has got a little 5" Knight which I knitted and a wooden dragon so he plays Saint George a lot. He has asked me to make more knights.
He has also got a little King, farmer doll, and gnome dolls of around that 5" proportion-he is very happy with these "hero" figures, especially since they've got little horses.
His other favorite things which get almost daily use:
blocks and logs
wooden tunnels (in the elements shapes)
wooden garage with road
little farm animals
baskets and buckets (for filling and toting things around).
hats- amazing how he can transform with just a hat!
ETA: to hype up more "Waldorfy" characters- all we've done is read him lots of stories with knights, gnomes, etc. and he loves them, and goes and plays it out.