While Doctor and First Aid can cap nicely at 100%, other skills benefit greatly from exceeding 100.
Barter, in effect, doesn't offer you equivalent value at 100% proficiency. The truly obsessed trader will need very high Barter proficiency and, in all likelihood, an additional Perk to improve prices.
Melee, Unarmed, or any other combat skill at 100% will offer you the maximum possible chance to hit only if your opponent has used all his AP, is not wearing armor, and has no natural armor class from agility. Believe it or not, this means you won't have a maximum-possible hit chance against deactivated robots. (Note: Some armors mitigate damage well but deflect it poorly.) In order to reliably strike an armored opponent, you may need 130% by the late game. In order to ignore armor reliably, you may need at least 160%, but that assumed called shots, such as to the eyes. Simply hitting high level opponents is sometimes a matter of respectable skill.
Many non-combat plot solutions are available only with very high Science and/or Speech skills. By 'very high' I mean above 100%.
Other examples exist. I should try to figure out which is which and make something of an inventory, but at present I'm quite busy. I hope this helps.