might want to read a couple of the FAQ's and Wiki's on the game before posting, there are a ton of different features in the game that use "iconic" words from D2. Runes, Cauldron of Jordan, etc etc
Runes look to be extremely valuable though, and will pretty much be something you'll *always* be wanting/looking for. They have levels, and finding the next level higher rune (like gems were in quality), will immediately make the skill you put it into whatever % better. They pretty much moved everything having to do with your character's "spec" into these runes.
But you never know what they'll do in an expansion, there weren't runes in classic.
Enigma was one of the most interesting additions to Diablo 2 in its long lifetime. The item-only skill model was simply awesome, but it brought a little too much to the table for the superwealthy willing and able to acquire one. If they executed it better, but still kept it interesting, they should have even more item-only skills in D3.