just food for thought:
wolverine's fought hulk more times than spiderman's thrown down with:
carnage,
morlun,
absorbing man,
shocker,
kingpin,
morbius,
and a handful or two of other spiderman "villains", hell he's fought hulk more times than spiderman has fought some of his villains combined.
the real problem here is that we really do need a definition to describe what a personal rogue, or personal villain really is.
to the point on hulk and magneto, both are obviously portrayed as rivals of wolverine. Cresh was absolutely correct in his assessment that hulk (more often than not... and not professer hulk, since prof, hulk actually constituted that he liked wolverine) hates wolverine, or "the little man" as he's come to call him. Marvel has pretty much come to the conclusion that wolverine vs. hulk is one of the best selling/most popular grudge matches in comics. For magneto, the previous statements were also correct in that magneto reveirs wolverine as his "most respected foe". I interpretted this to equate to magneto having a respect for wolverine's sense of honor, assertive nature, and realistic attitude. However I can understand how people would argue that magneto appears as a wolverine villain. Just look at x-men 25... the consequences of what magneto did to wolverine effected him for the next half a decade in his comic book career. Magneto has personally ripped the admantium out of logan's body, logan personally gutted magneto, wolverine personally took off magneto's head. The cause/effect relationship that the two have (at a personal level) is something that seems to be far more substantial than that of the cause/effect relationship spidey shares with most of his villains. While it's true that wolverine's rivalry with magneto has stemmed from his participation in the x-men, it should also be considered that simply because there are other bystanders present during confrontations between the two, the genuin and PERSONAL nature of their rivalry is no less prevailent. While I wouldn't consider magneto a rogue of wolverine's, they are however consistenly at odds, hence, rivals. I personally agree that magneto isn't a wolverine rogue, but he IS a rival, as is hulk (and thus far the arguments against hulk have generally been cop-outs... but I'm open to a good argument).
to the question at hand.. (as I said before, we really need a definition here to properly debate the issue, until then I feel we're arguing over nothing in a sense)... off the top of my head, I think this is truly a tough decision. While in terms of h2h, I certainly give the spidey villains a major edge. Wolverine faces off against great fighters with lots of durability and stamina, but spiderman's villains almost always need a plot device to be beaten in a strait up brawl. The MAJOR problem for the spidey villains though is that wolverine has a large portion of his own villains that are mystical in power. Ogun for instance could potentially off the entirety of spiderman's "rogues" with relative ease. gorgon could just take off his sunglasses and that's half the fight over right there... there are too many variables to debate this properly.
we need
1) a definition of "rogue". and...
2) perhaps a certified list of villains (that everyone can agree on) for each character for easier assessment.