we use the uniball 'vision exact' pens in micro and fine sizes, in our office. can't say that they're my favorite, but they're free so i use them. for sketching i like the 'micro' size in black, and for the thick lines i use a felt-tip Pentel Sign Pen.
also i use sharpies, but not for writing notes as they bleed through. i like the way they smell.
i fill out forms with blue ink. i mark up drawings with any color except black - usually red, but sometimes green or blue.
for good drawing, i like the sakura pigma microns:
i'd like to develop a good color-coding organizational strategy for my work notes. does anyone know of a system? dates, meeting notes, action items, phone notes, research, etc. ....would be good if it were limited to 2-3 colors, as i can carry two pens in the spiral of the notebook.