Personally, I don't think they have bad album, and they are all great for their own reasons (I've said the same about Tool's albums, I know). And picking a favourite album isn't necessarily an easy task. But if I had to choose which SOAD album I'd like to be trapped on a desert island with, it'd be Mesmerize. To me, Mesmerize is the highest point of the bands career. With their earlier material, you have this "untamed" beast, so to speak, called their debut album. It's wild, strange, loud and a teenage rebellion's wet dream. As they began to release albums such as Toxicity and Steal this Album! (B-sides, I know), they began to refine their song writing more and more. With Mesmerize, you have an album that combines the obscurity and hardcore influenced elements we heard from their first few releases, but with a much more fine tuned style of writing and flow within the music. The album itself just seems much more...well made. As if it really took an immense amount of time and effort to make, whereas their earlier work (While great, I'm not talking down towards their older albums at all) felt a bit more unpolished and recorded "just for the fucks sake of recording an album".
inb4 teh flames