JRuby is one of the most complete ruby implementations (there are a lot other ones out there such as IronRuby, Maglev, Rubinius, XRuby, YARV, MacRuby). It is very comprehensive, therefore, unless you use gems that use native C code, you will very very likely be just fine compatibility-wise.
JRuby is a bit faster than the actual C implementation, but it supports actual threads, whereas the official implementation is struggling a bit into getting it (it still uses Green Threads). Using Java threads from JRuby is quite trivial, even though it will require you to couple your code with Java (with a little DI, this coupling will only happen once, though).
Another benefit: runtime tools. Java, as a platform, instead of a language, has a lot of runtime tools to help you diagnose problems and check the state of the application (profilers, JConsole, and so on).
Twitter engineers also mentioned that the Ruby VM kinda has trouble being an environment for long lived processes, while the JVM is very good at that, because it’s been optimized for that over the last ten years.
Ruby also had a little security issue recently, which did not affect JRuby's implementation.
On the other hand, your project requires more artifacts (JVM, JRuby jars, etc). If you are using an application that will stay alive for long, and you want better runtime support, JRuby can be a great way to go. Otherwise, you can safely wait until you need these things to actually make the move (it is likely to go smoothly).