What's the piece of wire in the tool pouch for?

[auraaura]

It's about 4-5 inches long with a loop on each end. I can't figure what it's supposed to do..?

[Guest branthopolis]

Its to lock your helmet to the bike..  Loop the wire through the helmet D-ring then the other end attaches to the hook under the seat..
 
 

[db5304]

I've also seen it mentioned on here that it would be better suited as a cheese cutter.  I've used it before and it seemed decent.  It is a tight fit so I don't think you could get something in there to cut the cable, but it does make it a bit tricky to get the helmet there.  

[auraaura]

OK. Now I know. Thanks! (cheese cutter :-)

[jimf]

It is a tight fit so I don't think you could get something in there to cut the cable, but it does make it a bit tricky to get the helmet there.  

I think it's only long enough if your helmet has a D ring strap system.  My Schuberth uses a ratchet latch instead.  You could run a wire through the chin bar but the Yamaha wire is nowhere near long enough for that. 
I thought about hitting my local hardware store for something more useful but am so lazy I just always take the helmet with me.  I don't really want to leave the Sena out in the breeze anyway.
 
 

[steveb]

It is a tight fit so I don't think you could get something in there to cut the cable, but it does make it a bit tricky to get the helmet there.  

I think it's only long enough if your helmet has a D ring strap system.  My Schuberth uses a ratchet latch instead.  You could run a wire through the chin bar but the Yamaha wire is nowhere near long enough for that. 
I thought about hitting my local hardware store for something more useful but am so lazy I just always take the helmet with me.  I don't really want to leave the Sena out in the breeze anyway.
 

I ended up getting a lightweight (though much more substantial than the Yamaha supplied wire) bicycle cable w/ combination lock.  I thread it through the center of the handlebars and the chin piece of my full face helmet.  No worries of someone just cutting the helmet strap and walking away. 
 
 

[jimf]

I ended up getting a lightweight (though much more substantial than the Yamaha supplied wire) bicycle cable w/ combination lock.

Be aware that most of those locks can be opened in a few seconds just by playing with the tumblers.  I used to do that as a party trick when I was in college; close my eyes and open the victim's lock inside of 30 seconds.  The really cheap locks could be defeated in 10-15 seconds. 
How long it takes mostly depends on how good the lock's manufacturing tolerances are, so the more expensive locks were certainly more resistant.  I can't say I've tried any of the newest round of expensive locks, but I haven't ever had one defeat me for more than a couple of minutes to date.  As a result I don't trust those for anything more than to be a visible deterrent, keeping honest people honest.
 
Having said that, if you're running the cable around something under the seat then you could lock the cable lock under the seat and it won't be accessible to the would be thief at all.  Then any cheap lock would be fine.  Heck, given a cable with two eye loops you might even be able to use the hook that Yamaha provided for their own cable without an extra lock.  I did that once on an older motorcycle which had a helmet D-ring hook under the seat, but haven't yet looked to see if it's feasible with the FJ.
 

[bobaintstoppin]

I'm using a lock similar to this:
http://www.aerostich.com/retractable-cable-lock.html
 
As JimF says, likely easily defeated by a dedicated thief, but it keeps the honest people honest.  I loop around the passenger hand hold and through the chin bar of my Arai.  Works easy.

[estell]

 I loop around the passenger hand hold and through the chin bar of my Arai.  Works easy.

A gun lock works well too.