it's kept in throttle.dat in your settings dir.
exactly WHEE this dir depends on:
Where you have rutorrent installed
Whether or not you use some form of authentication
If so, what the username is.
For instance, if you use authentication, have rutorrent installed at /opt/webstack/http/ and have a username wonslung it would be at:
/opt/webstack/http/share/users/wonslung/settings/throttle.dat