Don't know how modular your project is.

I think it does not matter if it is just one module or if it consists of many components if you choose a good OO design.

I write tests for every class/module with the standard tool for the language (Test::More on Perl,JUnit for Java,...) because they are well documented (good for other developers) and mature.

for example if Java component X does the main calculations and Perl Module Y uses some of this Java libs, then test in X with JUnit that the calculations are correct and in Y with Test::More that the communication is ok.