Okay, so I realise this sounds rediculous. It did to me, too, at first. It almost seems impossible for Spider-Man to overcome Iron Man's armor and weapons, but I came up with a way that he might just be able to do it.
Imagine this: Spider-Man is confronting Iron Man for some reason, and is very angry (And wont hold back). Iron Man scoffs, believing it impossible for Spider-Man to beat him in any kind of fight (Think Civil War). Spider-Man lashes out, Leaping for Iron Man with his fists balled furiously. Iron Man easily evades the attack and blasts a repulsor ray out at his foe. Spider-Man uses his Spider-Sense to dodge the beam, and webs up Iron Man's palm, overheating the repulsor before he can fire another beam. Iron Man activates his suit's flight ability to gain some distance while he prepares to continue his attack, but Spider-Man furiously webs up on to Shellhead's back, where he uses his amazing strength to begin to dissassemble Iron Man's armor. Spider-Man continues to beat down the now-vulnerable Tony Stark.
Keep in mind just how strong Spider-Man is (Think Scorpion's jaw) and just how effective his spider-sense is.