I know that for skills like, say, Destruction, and Marksmen, going over 100 is pointless. But for other things, like upping your Magicka, the more you have, the better. So what skills get a benefit from going over 100?

Acrobatics and Athletics continue to make you jump higher and run faster.

Increasing the attributes past 100 continues to give benefits. Intelligence -> Magicka, Strength -> Encumbrance and Fatigue, Willpower -> Magicka regeneration and Fatigue etc.

I see. So all the attributes, Strength, Intelligence, Willpower, Agility, Speed, Endurance, are worth getting over 100 then? And what of Luck and Personality? Also, I know that if you fortify Mercentile to...what is it, 75? That you can invest in shops. Unlike other skills, you don't have to raise it up to 75, you can just fortify it up to that. Are there any other skills like this? That you can fortify up to a certain point to gain the benefits? (Like Fortifying Marksmen to 50 so you can Zoom in.)

How do you get these attributes over 100?

Perma-enchanting.

The Mercantile investing perk being given for a fortified level is something UOP fixes - that's possible because it was controlled by the dialog condition for the investing option. All the other perks (AFAIK) are coded into the game engine and aren't affected by the current effective level, just the base.

Levels can go past 100 any time a "Fortify x" enchantment is in effect, whether it's because of an item you're wearing, or an ability, or spell (or by curing a disease / removing damage that reduced it).

Ah, I see. That makes sense. Thanks Ghastly.

I have 100 blade enhanced to 125 or whatever with some gear. I am hoping it makes a difference when chopping up. In fact believe it or not the only challenging battles I get lately are 2-3 goblin warlords jumping up and down.....

As mentioned above acrobatics above 100 will let you jump higher, athletics above 100 will let you move faster. All other skill have no benefit over 100.

Attributes do have a benefit over 100, in general:

• Speed - faster movement (running, swimming)
  
• Intelligence - more magicka
  
• Willpower - faster magicka regeneration (except for an Atronach), and more "fatigue" (aka stamina)
  
• Endurance - more health, more fatigue
  
• Agility - more fatigue, but no additional bow damage. It is unclear if this will affect sneaking or lockpicking. It seems to me that it doesn't but there are some contrary claims. This seems unresolved.
  
• Strength - more fatigue, higher encumberance limit, but no additional melee damage
  
• Personality - maybe a higher starting disposition, but it really doesn't matter
  
• Luck - affects a few misc things like Mehrunes Razor

Sorry it doesn't help 125 Blade = 100 Blade.

What Savlian said, Any skill like that, Blade, Destruction, Blunt, Hand to Hand, ect ect, over 100, doesn't help it.

Also, thank you for explaining the attributes. I kind of figured that enhancing those would be a good thing to do past 100. (Not needed exactly, but it does work, which is what I was wondering.)

Other than acrobatics and athletics, as mentioned already, I don't think there are any other skills that benefit from going over 100.
I'm uncertain about speechcraft and sneak.
With 100 speechcraft, I believe the highest you can persuade someone's disposition toward you is 90 (without having your weapon drawn). I don't know if that changes with higher than 100 speechcraft.
I'm also curious if going over 100 sneak actually makes your character any harder to detect.