Updated August 31, 2011
This thread is meant to serve the community, not myself, so if there's something you'd like to see being done differently with this, feel free to discuss it with me. Be sure to post your suggestions (with links) so I can add it.
Also, be sure to check out the Gigathread, an index of megathreads to also post your ideas in.
This thread is divided into sections based on what kind of ideas it is, as well as being alphabetized in each section:
Natural Blocks and Items, Terrain, Ores, Caves, Mobs, New Realms, and all of Nature
Crafted Blocks and Items, New uses, Redstone, Tools, Workstations, Minecarts and all Player made Stuff
GUI, Interface, Game modes, Abstract concepts, Graphics, and Miscellaneous