I have a large quantity of gyro values and I read them through the Arduino serial monitor. I'd like to know how I can use these values in other programming languages (such as C/C++/Java) after the values are read. Are there particular libraries for the Arduino that could help me in this way?
Yes, of course you can.
In C/C++ there are different libraries depending on your operating system - that is if you even really need a library to help you at all (in Linux you certainly don't - you just use standard system calls - open, read, etc).
In Java there are a few different ones. RXTX is a common (though not very good) one. Personally I ise JSSC(Java Simple Serial Connector) since it contains the JNI files for all the main platforms - you don't have to get the right separate library packages for your specific OS like you do with RXTX.
Then of course there's things like PySerial for Python, Device::SerialPort for Perl, and whatever nonsense Microsoft have created for C# and their .NET stuff.
So in general: pick a language you are comfortable with, then ask Google how to use the serial port in it.