Very recently having been in a similar situation as you, I've decided to:
- Use Java for the time being
- At the same time keeping an eye on the progress of the D programming language.
I'm going with Java, since as somebody pointed out, there's really a lot of tools already available in Java, Java has over the years come to have very good speed (I've heard things like 90% of the speed of C/C++ code), and you get going much faster since you have garbage collection and a much cleaner language than C/C++. (Also Eclipse is a great platform, on which you can build interesting, very modular stuff, such as Bioclipse)
I keep an eye at D, since from almost everybody I hear it is a great, clean and powerful language, that fixes the annoying flaws in i.e. C++, while still being a compiled (and thus potentially fast) language. Like Java, it has garbage collection, but the syntax is said to be even cleaner than that of Java, plus you can do really close-to-the system programming/optimization (even write inline assembler code) if needed.
(Much of this, you can read in this question on D, here on BioStar)
Finally a word on python: I think python's ability to compile to C-code with just the addition of typing the variables, with the Cython package, is very neat, and might solve many performance-demanding tasks, if you have reasons to stay in the scripting-world.