HA>I'm curious to hear some thoughts by other authors on using Japanese 
HA>language in fanfics, and what the best way to let the reader know 
HA>what the words mean, if (s)he doesn't know them already.

This may be well and good, but can be confusing for
people who are just getting into fanfics, or those who
don't care much for Japanese. To stay safe, I suggest
at least keeping a glossary at the end of the file.

It can be less obtrusive than inserting a note immediately
after the Japanese phrase, but isn't as convenient. 
However, if you really want to support this movement, it
would be a good idea to keep the meanings at the end
so that the readers will be forced to remember the lines. ^_^

HA>"Kuso!" he swore angrily.

In this case, it is easy enough to gather the meaning 
from context. However, it would still be a good idea
to keep the meaning at the end, if you're going to
keep a glossary anyway.

HA>"Motto hayaku, Tenchiiii! Motto hayaku! Iki-soo-daaaaaaaaaaa!" :)

??!? More, Tenchi!!! MORE!!! I'm coming!!! <is that how it goes?>