Mmm, it's been an obscenely long while since I played, but here goes from my hazy memory:
1) Age of Shadows, in addition to a new landmass and customizable housing, introduced the Paladin and Necromancer skills and abilities.
2) Dragon Scale Armor - Skin a dragon (or related creature) and you'd get a few cornflake-looking items which could be made into armor. The resistances varied with the scale color.
3) New Weapons and Armor Crafting - Based on the metal used, these items would have varying strengths, resistances, and weaknesses.
4) New Weapons and Armor - Among which were slayer weapons (and I think instruments as well) that were extra effective against a given class of creature.
5) Magic jewelry and clothing which beefed stats and skills while worn.
6) Stat scrolls - These items could applied to select skills (and abilities I think) and raise them over the normal cap in increments of 5. For example, one blacksmithing scroll could raise the skill cap to 105, while the maximum could up it to 120.
7) Other new craftables and craft-enhancing items - Tinkers of a certain level could build controllable golems to serve them or others after gathering the right materials. My craft mule absolutely loved those suckers when he'd pull ore elementals using a gargoyle pick. Spam "all kill" and haul ass out for cover, then creep back and repair the mechanical beasts

.

Plant quests - Growable rares that you could grow from one generation to the next, crossbreeding as needed to get the rarest permutations of color and type.
9) A great quest that would net you a nifty little bag. If the bag was charged up with powder from a related quest, you could use it to send items directly from your pack to your bank box (as long as space was available, of course). Not particularly abuseable, since the bag was a "no bless" item and held limited charges before it was drained and needed recharging. (The powder quest was fairly involved, so it took time to get a full amount.)
Now I'm sure some of this is spotty and possibly wrong, but those were the only ones I could remember off-hand.