Greate article on analyzing jQuery vs MooTools, even has an dedicate URL:

jQuery vs MoolTools Chart

For my opinion, I don’t know why people like to put these two javascript framework to compare (or prototype.js etc). Each of them has its own scope: jQuery is easy since it has a lot of plugins therefore it is good choice for people who want to focus on product. MoolTools is more powerful in nature design, so it is good for serious programmer especialy for OOP. If you are using RoR, than use Prototype.js since it is originally design for RoR.

There are no BEST choice in this world, only a better choice, depends on your target or scope.

By the way, if anyone wants to know, I use jQuery.