2 questions

[shinningman]

1. Where can I find a list of ladder only runes?

2. Why do people trade perfect gems for items on battle.net?

[Are]

All runes drop in ladder, open, and single-player. If you want a list of ladder-only runewords, you can find them here:
http://www.battle.net/diablo2exp/items/runewords-110.shtml

The list of ladder-only runewords starts about halfway down the page.

Perfect gems are traded for items because they are needed for some very useful cube recipes (rerolling grand charms, for instance), and are less likely to be duped than other currencies used (such as HRs).