I learned D&D from the 3.0 Monster Manual; haven't seen that beat.
My next favotite MM is MM3; which has the best monster selection, mechanics, and layout of any of them. After that MMV is creative but has a lot fewer monsters, more wasted space, and less classic fantasy types.
Almost the entire specific monster line is fantastic (LM, Draconomicon, FC1&2, Lords of Madness). The one I use most is LM, because you can never have too many undead.
The environment books also have great monster sections.
Tome of Horrors (Revised) is the best 3rd part monster book I have, for sheer breadth of selection.