yamete - stop that!
shizuka ni - be quiet!
OK? - (obvious, but I usually use it in the context of "Do you understand?")

For the first two, those are usually a last ditch effort when English isn't working and the JTE isn't stepping in to get control.  I try to very rarely use Japanese.  Also, a very loud, "SHHHHHHH!" is usually enough to get them to quiet down.  Or one time when I had a particularly rowdy class I picked up an encyclopedia and dropped it on the desk.  That had them quiet real quick ;)

I don't want to be a nit picker, but "kite kudasai" should be "kiite kudasai". I only say something because otherwise the students might be confused if you don't elongate the "i" long enough as it will sound as if you're asking them to "come here" instead of "listen".

yamete - stop that!
shizuka ni - be quiet!
OK? - (obvious, but I usually use it in the context of "Do you understand?")

For the first two, those are usually a last ditch effort when English isn't working and the JTE isn't stepping in to get control.  I try to very rarely use Japanese.  Also, a very loud, "SHHHHHHH!" is usually enough to get them to quiet down.  Or one time when I had a particularly rowdy class I picked up an encyclopedia and dropped it on the desk.  That had them quiet real quick ;)

urusai - litt. means noisy, but the equivalent to "shut up!"

(I would only use that if you are WAY pissed though.)

kite kudasi - Please listen 

I find "Oi!" to be rather effective . . . cannot offer an explaination for that though . . .

I don't want to be a nit picker, but "kite kudasai" should be "kiite kudasai". I only say something because otherwise the students might be confused if you don't elongate the "i" long enough as it will sound as if you're asking them to "come here" instead of "listen".

and if you "kitte kudasai" them they may just start cutting...

I also find that it is not so much what you say but how you say it. Use your voice tone, body language and facial expressions. I have become very good at the 'You don't seriously think that you can do that in my class" stare...works very well. Sometimes using a soft gentle voice also is effective though you have to pick the right situation for this. This only started working once I had built up a relationship with my kids.  Also the less you use Japanese, the more effective it will be when you use it. When I use it I am normally fed up and so say things like "shaberanai" or "kikinasai". Also, when in doubt, listen to what the JTEs say when they have had enough. That will give you an idea as what you are able to say without 'crossing the line'.

I taught myself how to taxi whistle really loud and that got the attention of some crazy classes.  But they mostly just stopped to say, "sugoi!" and then went right back to being noisy again.  And also my fingers tasted like chalk. 

I think if you have to say something in Japanese to get their attention, say "kiite kudasai" (please listen) or the command "kikinasai" which means the same but is stronger because "-nasai" is used to give a command to someone lower than you in the pecking order, like children or students.  So, it's better to tell them to listen rather than tell them they're loud, or to shut up.

I agree with Megs; attitude in your speech makes a big difference.  It's important to make sure kids don't think they can walk all over you (as they do with some JTEs), but showing a lot of anger toward them could actually make things worse.  The big reason is because of the language barrier between the ALT and the students.  Not only is it hard to communicate verbally, but culturally it's hard to read people and decide whether or not they can take what you dish out.  Since most kids are not used to receiving much discipline from angry teachers, they won't know how to respond to an angry ALT.  I think it will just make the communication barrier thicker. 

I have dealt with loads of punky kids--whom I really do like!--and I think if you show them that you really like them and don't think they're all jerks (think: kill them with kindness), they'll be less likely to give you guff when you really do have to tell them to knock it off and be quiet.  I think if they feel that they are already on good terms with you, then when they act a fool and you have to give them a disappointed look, they'll know they just went from cool to uncool and will hopefully shape up...for the moment, at least. 

And, as I was once advised, just plain ol' outcool them!  Especially junior high kids.  We're already cooler than they are, so why not just play off that?  You're seriously cooler to them than you think you are.  Coolness goes a long way!  Hahaha...