...are worthless. All of them. And they're ridiculously expensive. Or is it just me?

Not really worthless... but definitely too expensive. There is currently an unorganized movement to convince Riot to remove dedicated Energy runes and add them on to the Mana runes ala the Expanded Mind mastery. This wouldn't happen until the Great Rune System Rework, which as far as we know has not even started yet. Hippalus has stated that if he were to reconsider the rune system (&rune combiner) that wouldn't be started until after season 3 started; so it probably wouldn't even be ready until at LEAST halfway through season 3, if not the end or saved for the "big patch" starting Season 4.

Well, all the energy-based champions have 200 energy and 50 energy regeneration per 5 (or 80 energy regeneration per 5 with blue buff).

You can get up to 42 extra energy if you get energy per level and flat energy, or 36 energy with just flat. With energy regeneration per 5 you can get another 10, or 15 if you invest in the per levels. So, you can increase your energy pool by 18%-21%, and/or increase your regeneration by 20%-30%, which seems somewhat substantial.

Only problem the runes run into is weather or not you actually run out of energy often enough for them to make a difference. With Akali, that's generally not going to happen. I've heard with Shen and Lee Sin it can be problematic though, so with those champion you may want to play around with the energy a bit, if you have the IP to afford them. For a rather niche rune that only effects 4(?) champions, they are obscenely expensive though.