Answers

1. Missing bird

2. Extra finger on Alyx

3. Alyx's tooth missing (she got into a drunken cat fight with Dr.Mossman)

4. Gordon's "Laser Beam" is a little bit shorter in this picture than the other (Barney - "It's not a laser! It's a little lightbulb that blinks!")

5 (and 6). Gordon's sexy green eyes are a shade of blue in one of the pictures.