Please don't use kill -9 indiscriminately, it's a very bad habit.
The correct command is
 $ adb emu kill
Or I should better say it was the correct command until some recent adb changes. It seems somebody forgot to add the authentication to it.
In the latest (as of June 2016) the latest adb version is
$ adb version
Android Debug Bridge version 1.0.36
Revision 0a04cdc4a62f-android
and when you try
$ adb emu kill
nothing happens, and this is why
...
connect(3, {sa_family=AF_INET, sin_port=htons(5554), 
sin_addr=inet_addr("127.0.0.1")}, 16) = 0
write(3, "kill\nquit\n", 10)            = 10
read(3, "\377\373\1", 8192)             = 3
read(3, "\377\373\3\377\373\0\377\375\0", 8192) = 9
read(3, "Android Console: Authentication required\r\nAndroid Console: type 'auth <auth_token>' to authenticate\r\nAndroid Console: you can find your <auth_token> in \r\n'/home/diego/.emulator_console_auth_token'\r\nOK\r\n", 8192) = 202
read(3, "k\33[K", 8192)                 = 4
read(3, "\33[Dki\33[K", 8192)           = 8
read(3, "\33[D\33[Dkil\33[K\33[D\33[D\33[Dkill\33[K", 8192) = 28
read(3, "\r\nKO: unknown command, try 'help'\r\n", 8192) = 35
read(3, "q\33[K\33[Dqu\33[K", 8192)     = 12
read(3, "\33[D\33[Dqui\33[K\33[D\33[D\33[Dquit\33[K", 8192) = 28
read(3, "\r\n", 8192)                   = 2
read(3, "", 8192)                       = 0
close(3)                                = 0
exit_group(0)                           = ?
+++ exited with 0 +++
Then we need another solution.
If the previous command does not work (as some users reported for Windows) you can try (in the next command 5554 is the port used by the emulator).
Copy the content of the token file (~/.emulator_console_auth_token) to the clipboard so you can paste it during your telnet session:
$ telnet localhost 5554
Trying 127.0.0.1...
Connected to localhost.
Escape character is '^]'.
Android Console: Authentication required
Android Console: type 'auth <auth_token>' to authenticate
Android Console: you can find your <auth_token> in 
'/home/user/.emulator_console_auth_token'
OK
auth <YOUR_TOKEN_HERE>
Android Console: type 'help' for a list of commands
OK
Android console command help:
    help|h|?         print a list of commands
    crash            crash the emulator instance
    kill             kill the emulator instance
    quit|exit        quit control session
    redir            manage port redirections
    power            power related commands
    event            simulate hardware events
    avd              control virtual device execution
    finger           manage emulator fingerprint
    geo              Geo-location commands
    sms              SMS related commands
    cdma             CDMA related commands
    gsm              GSM related commands
    rotate           rotate the screen by 90 degrees
try 'help <command>' for command-specific help
OK
Then, you can just enter kill at the command prompt
kill
OK: killing emulator, bye bye
Connection closed by foreign host.
and the emulator will exit.
But wait, there should be a better way. And in fact there is!
This gist provides an automated solution using expect instead of having to cut and past the authentication token every time.
Hope you find it useful.