As with all Tool albums, for me It comes down to what mood I am in. I've never been able to pick a favorite. I love them all.
Aenima - Raw and pissed. Although not as raw as the two that proceeded it. A much more fleshed out and ambitious album. As a kid I thought the transitions were cool, but as adult I skip them. This album has probably my favorite Tool song, which is the Title track.
Lateralus- Much more introspective, much more subdued and I've heard it referred to as "heavy pink floyd" and I can dig that for sure. Excellent album overall. Disposition and reflection are two of my favorite Tool songs.