In Oblivion, reaching various stages of skill levels grants special perks, for example, with weapon skills, for example, gaining higher skill levels unlocks new power attacks. Reaching one hundred in any skill just gives a perk that is usually better than the ones from lower levels. As for New Vegas, raising your skills to one hundred doesn't really give any special benefits you wouldn't get from using items to increase them to that level instead, as far as I know. Still, I generally make a habit of only using magazines for things like skill checks during speech, for picking locks or hacking computers, or for special actions that require a certain skill level. So while for skills like science and speech, I might consider leaving them at 90 and just using magazines when I need 100 skill points, if it's for skills like guns, I wouldn't leave it at 90 just because I can use magazines to raise it higher. Although I might not raise it to 100 anyway because it seems to me that with most weapons, you don't really need a skill level that high to be able to have pretty good accuracy.
Although, I don't think I've actually raised any of my skills to 100 yet, though I think my repair is pretty close. So I can't speak from personal experience, but at least I don't recall it doing anything special other than just generally making you better at that skill in Fallout 3.