I don't know any programming languages well either. I decided to program in C, since there are many applications still written in C, and I can learn languages as they came about historically...C being an older one, then C++, then I will probably learn Java. That's a while off though, I still need to get a handle on C before I move onto C++. I'm also learning some assembler along the way, although I'm not planning to write any big programs in assembler.

If your choices are C# and Java, I would choose Java. Java runs on many platforms seamlessly, has a large user community, has had a lot of the bugs worked out, runs fast and so forth. C# is kind of Microsoft-centric. I'm making sure my client is cross-compatible from the beginning - currently it compiles on Windows, Linux, Solaris and OpenBSD.