You'll find that a lot of words in Japanese can function both as onomatopoeia and regular words - ドキドキする (to be excited, nervous), キラキラする (to sparkle) - and that many others are mimetic - がっかりする (to be disappointed), びっくりした (to be surprised). If you look at a manga, you'll see effects like バタン (batan, thud), ガチャ (gacha, sound of a door opening/shutting), ドン (don, bam), ゴゴゴ (gogogo, rumble, an ominous presence) etc. pretty often. For an excellent sound effects index, see http://thejadednetwork.com/sfx/ - I use this website all the time for translating manga.

Hmmm, tough question. I don't think there are many. I do know one though, that's びり (Electric shock) I think that one is probably considered slang. Still a fun word though. :P