I chose Silent Hunter III over Silent Hunter 5. With GXW3 and SH3 Commander, Silent Hunter III feels like a lovingly restored classic car. It may not have the bells and whistles associated with a newer model, but it's solid, classy and very enjoyable.
I have watched a friend play Silent Hunter5, but I myself have not played it. My sense of Silent Hunter 5 is that it was an unfinished, buggy mess when it was released, and it initially required an internet connection to play it. The DRM component has since been removed, and the modders have done an awesome job enhancing the game, but looking at my friend play it, it feels like a game that doesn't quite know what it's coming to the party as.
As Jimbuna says, they are both cheap to buy, so try them both. I'll be staying with Silent HunterIII.
