Really, I don't think any shonen anime/manga has ever gotten it righter than JoJo arc 3. You have manly badass protagonists, a well-paced plot (seriously, this is the biggest feather in its cap -- even the most mundane of encounters keep the plot moving and keep the pages turning), creatively choreographed fights, and easily the greatest villain in shonen history. Dio may have been a little bitch in arc 1, but his performance in arc 3 really shows how he earned his massive Internet hype.
One Piece has really grown on me, which is really saying something given how insanely jaded I usually am. I guess it's mostly just hard not to love such a straightforward hero as Luffy -- no emotional baggage, no self-doubt, just a dumb but fearless berserker who stretches like chewing gum and doesn't afraid of anything. It is really hard for me to think of many other anime/manga protagonists I've actually wanted to cheer on over their villains. The art style is also pretty neat, so genuinely colorful and spastic.
And then there's Death Note. It's still technically shonen, but its gimmick really, really freakin' works. It's so nice to have a shonen series about a protagonist drunk on power rather than teenage moralfag #538-B embarking on a WACKY JOURNEY.