For writing on flip charts, I prefer the chisel-tipped, water-based Mr Sketch or Neuland markers mentioned above.

For writing on sticky-notes (super sticky post-its, etc.) or index cards, i hand out Pentel Color Pens (fine point fiber-tipped marker) in black and/or prussian blue. They are as readable as Sharpies, yet are non-toxic, dry instantly, and don’t bleed through the paper to mark the underlying notes. And less expensive. I purchase them in boxes of one color from http://www.artsuppliesonline.com/catalog.cfm?cata_id=1901. When you use these markers on notes, the notes are still recyclable.

I haven’t found any whiteboard/dry erase markers that meet my standards. All I’ve found so far are barely adequate. There are some that claim to be low scent or non-toxic, but I know people who still get headaches from them.