All the 3D was done in Maya and the 2D sequence was animated in After Effects, then it was all composited in Shake.

Great videos, I really like the 'They Live' one.

Funny that you call yourself a newbie after 2 years, but it's so true, I loved that job 'cause I was learning something new everyday (sadly the company closed down). I mostly work in AE these days, but I really miss my 3D work. Maybe I'll power up Maya a bit the next few days and see if I still know what I'm doing.