Okay, I'll make a list of all the things I can think of (however silly and tenuous) for and against and we can weigh them up. 'Evidence' in inverted commas because we know nobody has confirmed Nero's lineage properly, but these are hints and suggestions that point to either case.
'EVIDENCE' FOR NERO BEING VERGIL'S SON:
1. CAPCOM employee supposedly admitted he
was Vergil's son. Maybe he was kidding... maybe he was in on the designs that were supposed to reflect Vergil... I dunno. But technically he is in a better position to know what they were really thinking than we are...
2. DMC4 novel refers to someone who fits the description of Vergil being in Fortuna looking for history on Sparda, this leaves the gap open for his father possibly being Vergil, since his mother was assumed a prostitute and Nero is orphaned.
3. Nero has a vision in the novel of someone who fits the (vague) description of Vergil speaking to him about wanting more power. Not sure why he would have such a vision otherwise. And in the game, why would the exact same thing Vergil said be said to Nero in his head?
4. Dante states as much in the game that Nero is part-demon, and appears to have Sparda blood. Sparda was supposed to be dead before DMC3, so he cannot be a child of Sparda himself - he must either be a) Dante's son b) Vergil's son or c) Sparda had mysterious other children who could have fathered Nero, but this does not sound likely, given Sparda's supposed sense of honour and decorum. We are never told there were any other siblings in the Sparda family besides Dante and Vergil, but if there were supposed to be (apart from retcons) you'd think it would have been mentioned somewhere, either in the novels or the games. (If I'm wrong, someone please correct me, because I haven't read the novels).
5. Nero does not have the same powers of a half-demon like Dante or Vergil - or a full-body Devil Trigger. If he was only one-quarter demon, this makes sense it manifests in a different or less obvious way, localized to his arm (and the demonic aura).
6. Nero's DT does have the downward-pointing striped horns that Nelo Angelo had, and it is blue, and it's armour has similar patterns to some of Vergil's clothing from DMC3. I thought this was a reference to Vergil, rather than Yamato, when I played. If it is
meant to be a unique design, almost every fan out there who played DMC1 probably made the unconscious connection to Nelo based on the horns alone. Whether anyone thinks the DT strongly or weakly resembles Nelo, you have to admit, they could have made it look totally different from Nelo but didn't.
7. Nero's affinity for Yamato and its affinity for him (healing itself when it comes to him) could suggest it knew he was its rightful heir, and he felt comfortable with it. Dante also lets him have it, after stating he ought to 'keep it in the family'. This U-turn of opinion suggests Dante figured out Nero was his brother's son and lets him keep the sword because Vergil would likely have passed it on to him anyway (in addition to seeing that Nero is using it for the right reasons).
8. Fans suggest Vergil would have been too young to have fathered Nero. Possibly technically not, if you know what I mean - but also he could have visited Fortuna after the event of DMC while corrupted. If Sparda could walk about the human world in human guise and father kids, then Vergil more than likely could too.
9. Physical similarity to Sparda and his sons, white hair, etc.
'EVIDENCE' AGAINST:
1: Nobody has fully, "officially" confirmed that Nero is Vergil's son in a game.
2. The novel also could suggest Nero was injured and 'tainted' by a demon, hence developing the arm only after this happened, and it NOT being caused by inheritance. I would say the emphasis through all the games on bloodline being a prerequisite for demonic power makes this a stretch, but then look at Arius, or Sanctus, or Arkham... all of them are humans who managed to gain demon powers without any natural inheritance we're aware of. There's also the idea Nero was created by the Order - they
were doing creepy experiments with demonic power, and intended to use a Sparda son to activate the Saviour (if you disregard the novels which say he was an orphan).
3. The DMC4 novel states that the blue aura above Nero is Nero's soul. It doesn't refer to Vergil as far as I'm aware.
4. Fans suggest there would be little reason for Vergil to visit a prostitute or have children. Although not canon, Vergil's character in the manga looks down on 'painted whores' and it's not hard to imagine he wouldn't bother with them. He's too busy getting more power. (Then again, Vergil embraces his demonic side. So who knows?)
5. The quality of "wanting more power" might just be a general demonic goal, not one reserved only to Vergil. In that sense, whether Nero is Vergil son, the son of another Sparda relation, or even a creation, as long as he's got a little demonic blood in him, it's natural that he wants more power to protect Kyrie; he gets hold of a massively powerful Devil Arm (Yamato) and naturally wants to keep it. And there are plenty of mere humans drooling over 'more power' in the DMC series. . .
6. A lot of stuff is spin-off material, with vague hints and suggestions, but we can only really be sure if we hear the 'truth' in a game of the canon, or if a DMC designer comes forward and admits it is the case.
7. It's implied Nero is MORE powerful than Dante even, who is supposedly even more powerful than Sparda... for a quarter-demon to be more powerful than a direct son of Sparda is a stretch, but apparently it's true, so perhaps he is not Vergil's son at all. Why Vergil's son would be more powerful than Dante is anyone's guess, as it doesn't seem logical... (points to me more of him being a creation of the Order for use in the Saviour than being a descendant. Unless these CAPCOM guys just didn't swot up on genetics.
)
8. As mentioned by Darth Angelo, the scabbard of Nero's DT seems to be a feature of the Devil Arm Yamato and not of Vergil himself.
...If you guys mention some more I'll add them to the list.