I honestly believe SM3 had the best symbiote saga (although calling it a saga is a stretch and I believe this is most people's problem with it).
For one, Brock's motivations are the best depicted anywhere (with TAS very close indeed). We see early on he's very egotistical, unethical and really air-headed. And he goes on to lose his job, his reputation and the girl he supposedly "intends to marry", ALL by Peter's DIRECT involvement. Praying to God to kill Peter reaffirms all's not well with this guy, not many people would go that far. So it comes as no surprise that with a little nudge from the symbiote he gets totally maniacal.
Second, the symbiote really does make Peter himself quite bad, selfish and immoral. Here, dark Pete does not throw empty threats and doesn't simply yell at people. We see Peter taking care of all of his problems. He really puts his landlord, JJ, Eddie, Harry, Sandman AND MJ in their respective places. He even goes as far as to try (and basically succeed) and kill Sandman, throw a bomb at his best friend's face and humiliate and back-slap the only woman he ever loved. And the best part is that we can see what led to these actions, it's not that the symbiote simply made him evil. He had reasons to act like this even before the symbiote, which just takes care of any restraints he might have had otherwise.
Third, the central theme of the film about revenge seems the perfect frame for the symbiote story. Peter sees that he himself can get carried away with revenge and maybe go too far. And what is Venom if not the ultimate representation of a revenge-driven guy that just can't let go? Sandman provides Peter's focus for revenge and Harry is somewhere in the middle, going a little too far, but finally being able to redeem himself. It all fits nicely (unlike other random villains in other versions of the story) and gives the story a much deeper meaning than "We are Venom and we are badass"!
I even enjoyed the evolution of looks. Blue and red suit, symbiote covering the suit, adopting all the main characteristics with just a few alterations, and finally Venom's "twisted Spidey" look. It has a logical flow to it and leads to the best Venom look to date. Since Venom is essentially a twisted version of Spider-man, having his appearance clearly reflect that is a stroke of genius. Plus it's still quite faithful to his original look. Great production design.
TAS version is a very close second. It just loses points for making Peter suddenly and stereotypically evil and its overall kiddy and simplistic approach. The random involvement of a vague "prometheum X" and Rhino and Shocker doesn't help either.
SSM version I generally like for its more mature approach and dialogue, but they really dropped the ball with the maybe bad Peter (I know the symbiote affected him, but it was so subtle it didn't really have a point) and the very weak characterization for Brock, who in the end lost nothing at all, but ruined his future by randomly stealing the symbiote for himself.
The comics version didn't have the "behavior adjustment" angle, but I really liked the creepy feeling of a seemingly not alive organism trying to secretly take control. Most other versions (especially SSM) lost this feeling by outright stating the symbiote is alive. Brock's characterization here is also weak and random. Keeping in mind though that this saga was invented as they went and not planned from the beginning, it turned out pretty well.
I think Spider-man Unlimited speaks for itself.
I think that's all. You can start getting aggressive now...