No, they do not affect runes or gems. So sayeth the Arreat Summit:
What exactly are "Magic Items"
Magic Items in this definition include Magic Items, Set Items, Unique Items and Rare Items.
Magic find only affects what "color" an item is, after it is already determined what kind of item is to be dropped. Therefore, it cannot increase the chance that you get runes, gems, rings, amulets, charms, or whatever else. Those will drop completely randomly, based only on the drop tables.
Once an item that can have color (blue = magic, yellow = rare, green = set, gold = unique) is determined to have dropped, then magic find comes into play and helps determine what color that item should be. More magic find will skew the item results more towards the gold end of the spectrum.
No, magic find has no affect at all on rune drops. You are just as likely to get an Ist from a countess with 0% mf and 400% mf.
I do not know if MF has an effect on gems, I don't think this has been looked in to in as much detail as gems are fairly common, especially by doing the forge quest or farming the secret cow level.