Well i suggest to use Tamiya Weathering Master set. It's a set of three: Rust, soot and snow.
All of em can be applied to sub to give an aged looks.
Rust is of course obvious but you need to know where to apply them properly to enhance the realistic aged feels.
Soot can be applied especially to a modern sub model to darken the panel lines(hey coastal city waters are murky and obviously dirty)
Snow can be used to weather a modern sub lower hull to simulate a prolonged exposure to seawater. If you look at some modern sub pictures you'll notice that even quite a new sub has whitish lines/spots all over its lower hull(beow water line). But i don't think the withish lines extend to the upper hull of the boat as this part of the sub is often cleaned up.
As for WWII U-boat check this http://hsfeatures.com/features04/typeviicaj_1.htm
What i want to show is the chipped paint effect especially on the conning tower. I've some WWII film footage that shows u-boats returning from long patrols always show quite a bit of chipped paint on their conning tower. Because from what i saw in that film footage i think this u-boat link i give you perhaps is one of the most realistic in terms of having an overall chipped paint to its conning tower. Though the chipped paint is a bit overdone on the model.
Hope this helps