These are a few commands which i know work on the flash client.
/ignore
/unignore
/mode
/kick
/notice
/privmsg
To ignore someone you would do: /ignore nickname
To unignore someone you would do: /unignore nickname
The mode command can be done for multiple things like op/deop, voice/devoice someone, set a room mode or issue a ban.
Example: /mode #channel +s | /mode #channel +o nickname | /mode #channel +b *!*@hostname
To use the kick command you would do: /kick #channel nickname
To send a notice to somebody you would do: /notice nickname message here
To send a private message "PM* to somebody you would do: /privmsg nickname message here
If you need to use chanserv or nickserv you will need to know the exact command as at the moment the flash client does not show replies from them.