Obviously, we'd subtract any of the works that Newton contributed towards. Most notably: Principia Matematica.
So what does this change?
-Assume his work on Calculus was already done by Gottfried Leibniz. Thus this work on Mathematics is unchanged.
-Gravitational Theory. Newton took years to devlope the concept of gravity. It's not going to pop up any time soon. Certainly not until a genius like Albert Einstein. Maybe not even then. This was mostly due to Newton's look on science being influenced by his work on the occult. Remember that this was a view rejected by most modern scientists.
-Laws of Motion. I'm not an engineer, but I can only assume this would all influence future automotives, avionics, and submarines. Certainly, combine this subtraction to a lack of gravitational theory and any possibility of a space program disappears.
-Newton stabilized the British economy as warden of the Royal Mint in the 1690s. He put England on a bimetal system, and cracked down on counterfeiters. His work stabilized the British economy. How would a lack of Newton's economic efforts affect Britain's wars overseas, and could it butterfly away the American Revolution? Or would a less stable Britain only hasten a more violent revolution?
-William Chaloner creates phony conspiracies about Catholics to turn against the government. He would turn against the conspirators and profit from their downfall. Newton put Chaloner on trial twice, the second time finding conclusive evidence that he was engaged in counterfeiting. Without Newton on his ass, how greatly could Chaloner prosper? Maybe even starting his own colony in North America? (In OTL, he was hanged on 3/23/1699)