Showering twice a week is not enough, particularly if you tend to sweat. You should really wash every day; most people will start to smell a bit by the end of a second day after they have washed.
Not sure why your penis should smell particularly. What sort of underwear do you wear? More constricitive (tighter) underwear can make the groin sweatier and smellier.
If you are NOT circumsized, then you should definitely clean yourself every day and especially under the foreskin. If you are circumsized, you can let it go for a couple days here and there and shouldn't have any major problems...
I keep myself shaved down there... Not with a razor blade, but with a portable razor like someone would use to trim a beard. That keeps the general smell down because hair traps sweat and becomes a breeding ground for bacteria, fungus, etc. You have to be really careful and patient though, because you'll occasionally knick your sack with the trimmer and cause it to bleed a little -- it's not detrimental to your health but it'll hurt like a b* for a couple minutes! And the first few times you shave you'll get really itchy.. putting baby powder on afterward and before you put underwear/pants on will help to take the itch away.
It could also be a fungus, do you itch a lot? Maybe jock itch? ... Do you have any visible white patches or anything? A family member of mine had BXO, which caused a slightly visible fungus on the outside of the penis and some odor. It's sort of like a nasty yeast infection -- and his doctor gave him a dose of Difluconozole (spelling?) which cleared it up with just one treatment.
I'm not a doctor, but I would say... Buy a beard trimmer and shave it all off down there, down to the skin, every 30 days or so. After you shave, put on anti-fungal baby powder (like Medicated Gold Bond)... At least once a day, even if you don't shower, put some Cetaphil or similar product (it cleanses like soap but doesn't have to be washed off completely like soap does) on a washcloth and clean your penis and surrounding area. After it dries, put on the antifungal baby powder and fresh underwear. Change your underwear mid afternoon and reapply the antifungal baby powder when you do. Do this for a few weeks and see if you notice an improvement!