I've been struggling with this problem for quite some time as well and I think I've finally found a good solution.
I'm using Mac Bartender which is in free beta at the time of writing. The app has a lot of useful features for cleaning up an overflowing menubar.
For each menubar icon you can choose to:
- Display it normally
- Completely hide it
- Display it in the menubar when Mac Bartender is activated
- Display it in the Bartender Bar when Mac Bartender is activated
One thing to note is that it doesn't let you manage the built-in OSX 'menulets' (wifi, sound, spotlight, etc) yet, but that feature is coming according to their FAQ.
From the official site
Take control of your Menu Bar
With Bartender you can choose which apps stay in the Menu Bar, are
displayed in Bartenders Bar or Hidden completely.
Can be displayed and hidden as you want, by clicking on the Bartender
Icon or via a hot key.
If you want a really clean look and privacy, Bartender can also be
Menu Bar Apps still work the same
Apps still work the same when they are in Bartenders Bar allowing you
quick access to them when needed, but keep them out of sight when not.
Bartenders Bar can be placed where you want
Bartenders Bar can be moved at any time to any horizontal position
immediately under the Menu Bar. Or it can open under the Bartender
Menu Bar Icon.
Show an App in the Menu Bar for 5 seconds when it updates
Set up your Apps to be displayed in the Menu Bar for 5 seconds when
Hide Menu from left of Menu Bar to display maximum Menu Bar Apps
Bartender can remove the left hand side Menu temporarily to display
the maximum possible Menu Bar Apps in the Menu Bar.