I'm developing a web site that needs to get input from client's
microphone.  The way I'm doing it is using java to read from
microphone then send the data to my tomcat server.  To trigger the
code, I have to embed it as an applet in my html page.  This does not
work very well, since applets in general have problems running on
browsers.  As a result my app runs on most browsers, but there're
significant # of browsers failed to load my applet.

If I want to get around applet, can i use other languages and still
handle the request with tomcat?
1. flash - i know flash can read from microphone, but does it have to
talk to an rtmp server?
2. javascript - i wonder if java script can read from client's
microphone and make an url connection to my tomcat.  i doubt so, but
could someone confirm it.
3. java - is there anyway to trigger my java code not using an applet?
 or, even if i have to use applet, what is the best bet to make it
compatible with close to 100% browsers that have jvms installed?

If you want to use flash (and java in the backend), you can use Flash Remoting MX, 
which lets you communicate the flash application with a Servlet
running in the application server (your Tomcat could be enough).

More info about Flash Remoting MX:
http://www.onjava.com/pub/a/onjava/2003/02/26/flash_remoting.html

PD: it is not a free tool, I don't know the price I have only test the
demo version....