Is there any benefit to raising skills over 100 points with items? What about items/effects that add a percentage instead of a straight point boost? (e.g., you are 15% harder to detect when sneaking.)

Yes, it does indeed continue past 100. Even a fortify skill(as in not "two-handed weapons do x% more damage") like heavy armor increase the effectiveness.

Does the percentage boost apply to the skill or tje actual chance of success? For example, with a sneak of 50 and a percent boost of 15%, does that translate to an effective skill of 62.5? Or something else entirely?

It is additive. A 25% increase on a 100 skill would yield 125 skill rating. A 100% skill increase to 125 skill rating would equal 250 skill rating. The skill rating is not the chance of success of a skill, or the modifier. If you have 100 Archery, it does not increase your Archery damage by 100%. If you have a 25% Archery modifier, you do not deal 25% more damage with bows, your skill is 25% higher. The values are hidden from you so there is no real way of telling the exact amount of damage it adds. It is contingent on your skill, the enemy you are fighting, any buffs or effects, and your weapon.

Sorry, 62.5 should be 57.5. Doh!

So my vampire with a sneak of 78 and a skill boost of 40% (15% boots and 25% vampire) would have an effective sneak of 109?