1. What do I do with all these helium cells/spinmetal/wire/etc?

Primarily, these will be used for things like upgrading weapons. Common/Uncommon weapons tend to just require Glimmer to upgrade, but eventually you'll need these things.

2. How do I increase Intellect? None of these armor pieces do it.

You'll eventually find armor pieces that will.

3. Where/how do I get ship upgrades?

The ship lady in the hangar on the Tower will sell other ships. You'll also get a free ship at one point if you complete the story missions. The ship itself doesn't upgrade and is just cosmetic.

4. When will I find exotic weapons?

In a really long time. Haven't found any myself yet.

5. How do I get capes for my Hunter? (The ones Nathan Fillion peddles are up level 20)

Some vendors in the tower sell them, but they're really expensive. You'll probably find some randomly in loot chests, item drops, etc., as you play the game.

6. How/why/when do I use the vaults in the Tower?

If you have too many items for your player to carry, you can store them rather than discarding them. Also, you can share items between any characters you create using the vault--like Glimmer, the vault is shared between all the characters you create.

7. Is there a way to turn off the hit point counters above enemies?

Nope.

1. What do I do with all these helium cells/spinmetal/wire/etc?

These materials are used when modifying the more exotic weapons and armour in the game. You can also trade the materials in with faction leaders (including the Vanguard) for extra reputation.

2. How do I increase Intellect? None of these armor pieces do it.

I've found one piece of armour that increases Intellect; it's there, but appears to be very scarce.

3. Where/how do I get ship upgrades?

Rarely, they're in loot chests. You can buy them from the shipwright (for a LOT of glimmer) and one late-game mission gives you a new one. If you got the Limited Edition (or Ghost, which includes the LE) you get a code to download one; I think you pick it up from Tess's shop in the Tower.

4. When will I find exotic weapons?

Raids, Strike missions from the Vanguard playlist, buy them from faction leaders with Crucible or Vanguard marks.

5. How do I get capes for my Hunter? (The ones Nathan Fillion peddles are up level 20)

I finally got a (Rare) cape at about level 16 or so; I think it was a mission reward.

6. How/why/when do I use the vaults in the Tower?

Store stuff you don't need, to leave inventory slots available to pick up new stuff while on missions. Also, your Vault works for *you*, not a character; if you start another character, he/she can draw gear out of your Vault. This could be very handy.

7. Is there a way to turn off the hit point counters above enemies?

Sadly, no. I'm a bit disappointed Bungie had to use 'em too; much prefer how this was handled in the Halo games.

-- Steve dashed this off the top of his head, so some of the details may not be quite right... but the broad meaning should be close enough to work with.

1. What do I do with all these helium cells/spinmetal/wire/etc?

You turn them into the Vanguard Quartermaster and Crucible Quartermaster for Vanguard/Crucible points (to get cool gear).

2. How do I increase Intellect? None of these armor pieces do it.

Armor. I just recently got some blue-level armor that gives intellect boosts - I was probably around level 16 when I got it.

3. Where/how do I get ship upgrades?

The shipwright will sell you new ships. I am unaware of ship upgrades, at least to this point.

4. When will I find exotic weapons?

When you're finally approaching or at level 20 and above.

5. How do I get capes for my Hunter? (The ones Nathan Fillion peddles are up level 20)

Most of the ones for purchase in the tower are for level 20s. The main exception, and best way to get capes earlier is to buy encrypted class item engrams from the Cryptarch. For a few hundred glimmer you can usually get a class item from him which will be a random scarf or cape. If you don't like the one you randomly get, you can buy another and another.

6. How/why/when do I use the vaults in the Tower?

Access the vaults to store weapons that you either can't use for your character yet, or want to save for later, or want to give to one of your other characters. The stuff in your vault (and the glimmer you have in your inventory) is accessible across your three characters. You use the vault by opening it, then hitting the 'options' button on your controller and hitting the button on your controller that says "store" (I think it's the square on PS and the 'x' on Xbox, but I can't remember for sure).

7. Is there a way to turn off the hit point counters above enemies?

Not that I'm aware of... I personally wouldn't want to either -- the numbers popping off as you hit them give you valuable information about where to do critical damage, and what types of damage are more effective against each enemy (see: http://www.youtube.com/watch?v=uTLosBMLt3Q for a helpful explanation).

I think there were more, but that's a good start. Any assistance is appreciated!

Any time!