I don't think it's messy at all, I think it looks fantastic. I'm super jealous of that Batman TAS complete series box set, too.
That was actually my Christmas gift from my mother-in-law a few years ago if you can believe it.
I was tempted on picking up the LoTR Pez dispensers, at least I know you have good taste.
I actually have a huge LOTR figure collection in my attic. When my daughter was born I had to give up my extra room, so I only have enough room for the media. And barely even that as you can see.