On the latests versions of the Arduino IDE, in fact it is very easy to change the flags for any element of the toolchain, including the assembler, compiler, linker or archiver.

Tested on the Arduino IDE version 1.5.7 (released on July 2014),

Locate the platform.txt file,
AVR architecture => {install path}\hardware\arduino\avr\platform.txt
SAM architecture => {install path}\hardware\arduino\sam\platform.txt
Inside that file, you can change any flag, for instance,
compiler.c.flags for changing the default compilation flags for C++ files.
compiler.cpp.flags for changing the default compilation flags for C++ files.
You can also change any of the "recipes" or compile patters, at the corresponding section of the configuration file, under the title "AVR/SAM compile patterns".
After making the changes, you must restart the Arduino IDE, at least on version 1.5.7.
For instance,

To enable support for C++11 (C++0x), tested on Arduino IDE versions 1.5.7 and 1.5.8, you will simply add the flag "-std=gnu++11" at the end of the line starting with compiler.cpp.flags=".
It is expected that C++11 is enabled by default in the near future on the Arduino IDE. However, as of version 1.5.8 (Oct 2014) it is still not the case.