For static analysis of Java, the PMD tool (http://pmd.sourceforge.net/) can provide lint-like (or FxCop-like, depending on your exposure to these things) coverage of your source, with a configurable rule-set. It can generate its reports as part of an Ant build, and be integrated live into most Java IDEs to give live reports.
Like most of these tools, you will curse the first time you expose legacy code to it, and aim to clear the reports. In code that has to also play nice with .Net, you'll have to switch off two rules
LongVariable; and some of its rules e.g. about empty default constructors cannot always be all consistently applied (so may need case-by-case suppression).
To go along with the use of JUnit test, Cobertura (http://cobertura.sourceforge.net/) is a coverage tool that works by instrumenting the Java bytecode of the generated classes. It provides Ant tasks (and thus can be manually inserted into any Ant based build system, such as NetBeans projects) -- instrument the normal output in a post-compile step, and run JUnit against the instrumented code.
This tool gives you line and branch coverage reports like this sample -- all the way down from package-level summaries to line-by line indications.
While most of this post is about Java, I might as well add to the pot a 'C'-based tool, Splint, which, as the name suggests, is an uprated lint-style tool, which includes in its analysis some basic probing for code that might be vulnerable to buffer overrun -- at least in cases when a buffer is passed into a routine without any length, and then gets written to.
I've not managed to track down any good free tools for C++ -- Microsoft's Prefast (at least as of 2 years ago) balked when fed code containing STL headers; other tools are 'C' only, or pay-ware. Given the syntactic complexity of C++, this is not so surprising.