Blocks:

Red Mushroom*
Mycelium
Jungle Sapling
Jungle Leaves
Nether Wart*
Giant Red Mushroom
Giant Brown Mushroom*
Giant Mushroom Stem
Giant Mushroom Pores*
Redstone Lamp
Decorative Stone Brick
Iron Bars
Trapdoor
Mossy Stone Brick
Cracked Stone Brick
Diamond Block*
Tall Grass textures (Random Textures)
Cocoa Beans
Enchanting Table
Ender Chest
Pine Needles*
Fern
Brewing Stand
Brewing Stand Base*
Spruce Planks*
Jungle Planks*
Lava (Flowing)*
Lava (Still)*

Items:

Nether Wart
Bonemeal*
Spawner Egg*
Diamond Tools*
Magma Cream*
Bow Animation*

Mobs:

Iron Golem
Snow Golem
Cave Spider*
Ender Crystal
Most Randomobs alts*
Villagers*

GUI:

Enchanting Table Menu
Creative Menu
Hunger Bar
Hardcore Health Bar*
Experience Bar
Boss Health Bar
Server Status Icons
Title Panorama
Brewing STand Menu

Other:

Birchcolor.png
Foliagecolor.png
Grasscolor.png
Fogcolor0.png*
Skycolor0.png*
Myceliumparticlecolor.png
Redstonecolor.png
Stemcolor.png
Swampfoliagecolor.png
Swampgrasscolor.png
Underwatercolor.png
Tunnel.png
Glint.png
Mapbg.png
Mapicons.png
Lavadropcolor.png
Watercolorx.png

Rain
Moon phases
Custom Colors support
Random textures
All mod support except for TFC's Gem Pack

* = Major tweak/edit of existing texture