To the people who're making big long paragraphs on how Itachi would own Goku, or Goku would own Itachi, I'd like to say: STOP IT!!
That I did for laughs, actually. I think it's interesting how you're trying to defend your animes, but honestly, it's really not applicable.
I'd like to say firstly that Hash pretty much said it all. You can't compare the two ENTIRELY different animes. They both have entirely different "rules."
DragonBall/Z/GT: They're all powering up to super human levels that are so strong they destroy planets. They're extremely fast, and use attacks/jutsu (what have you) that are basically pure energy.
Naruto: THEY'RE NINJAS!!! That's it. They're just ninjas. Think about it. They're stealthy, not powerful. Fast? Yes, but not at the super-human-uber-omfg-power-up level. They have energy techniques, yeah, but they're tied in more to the spirit than.... whatever the heck you call what it is DBZ has...
About the only way the Narutonians could win would be in the scenario that they're fighting those from DB... cuz at that point, Goku is totally inexperienced, and Yamcha and all them are, pretty much, weak. Hell, even Hercule is STRONG enough to beat them, but he lacks the abilities (ki sense, bukujutsu [Alea, if I messed that up, I'm sorry], zanzouken.... intelligence) to actually make any difference.
The laws of each anime's universe would conflict... But if they were warped together, the Z senshi would win, simply because they're stronger, they actually FIGHT each other, rather than the ninja crap.
Note: I'm being very biased about each anime right now, but I lack the ability (at this point in time) to actually give you a deep explanation of it...