In our department the pens are quite mixed. My professor uses every pen that is in his reach (he gives them back).

I use a mechanical pencil with 0.5 mm B mines (HB is to hard for me, 2B to soft). I use no notebook, but for scribbling we have usually large stacks of printouts of previous versions of papers or the postscript code printed on paper (sometimes the printer drivers do not work). If things are more final I write them up in the computer (in LaTeX), then I can use grep and friends to find things.