I use nutritiondata.self.com. I am able to put in an entire recipe and see the breakdown per serving. I experiment a lot in the kitchen and was amazed by how quickly everything adds up when you throw a little of this and a little more of that into the pot.
I use cronometer.com for individual foods or if I'm faced with a dilemma while eating out. Thank goodness for my Paleo smartphone. =)
I've tried using different sites. I've been curious on levels of certain vitamins I get from the diet. I've found a few issues though. First off, accurately tracking them. It's one thing to have actual labels you can put in, but when using database entries often times this stuff isn't specified or even inaccurate.
Another issue is absorbtion. Obviously the easiest way is to just measure what we take in, but it's a very inexact way to determine how much of the vitamins we're actually taking in. For this reason, it's very difficult to directly correlate dietary intake, even if you have exact numbers, and use it to determine deficiency or supplementation plans.