Edit: Ok, I was wrong about the naming. A lot of the textures are quite hard to find. But if your file browser looks anything like this:
1. HD textures without MCPatcher! No more annoying people asking about the fire and portal textures in grass.
2. I don't need to update the terrain.png file whenever Minecraft comes out with a new block.
3. I can have custom animations without MCPatcher.
4. I can put a custom needle on my compass (Looks so much better without the glitchy super-thin needle).
5. Since I'm collaborating on the pack, I don't need to post a 1024x1024 image when I've only edited one texture.
6. More blocks/items can be added than would fit on a single texture sheet, without having to use even more texture sheets
7. When I save a texture as a psd, I can instantly convert it to png without copying/pasting into the terrain.png (minor, but about as much work as searching through an alphabetical list for a texture).
8. Making my mod will be slightly easier, because I won't need to worry about where each texture goes in the texture sheet to make it more organized.
9. The customizer I'm making for the texture pack will be easier, because I don't need to write code for putting textures in the right place in a texture sheet.
10. It's more obvious what each texture is for, because the images files are named.
11. Textures that haven't been created take up less space because I don't have to upscale a 16x16 texture, I just don't include the file.
12. For the same reason as above, unfinished texture packs could be slightly faster.
13. I don't see why I would, but if I wanted to I could mix and match HD textures.
Edit: Actually, sort of see why I would. I think 64x is perfect for a texture pack, but the compass is often used when held in your hand, and my custom needle looks a bit blurry because it uses anti-aliasing. I could make the compass 128 or even 256x, however, and then it would look much better.