The apps are the first to blame, but consider that they are (usually) 3rd party, aren't really policed by anyone and subject to poor design / development. Let's say one of the apps have a memory leak, or is a huge resource hog that affects the overall performance of the phone.
It's no different than a computer. If you spend $1000 on a PC, are you mad that you have to reboot it every once in awhile?
As the other poster said, take it back to stock. Also - be aware that we are on the first 4G phone for Verizon. Living on the bleeding edge is going to make you bleed yourself, at least a little. Being an early adopter of technology means you have to put up with some of the niggling issues that maybe weren't fleshed out in the design room.
Two days ago, I had to pull the battery from my Thunderbolt because the phone was acting up. After that battery pull, things have been fine.
It was the exact same thing with the Droid 1 when it came out. You just need some patience and be able to look at the big picture. If after some time you are rebooting your phone / pulling your battery daily on a stock phone - then yes - you have some problems.