You can convert your JARs into EXEs using Jarsplice or similar tools, but it is fair to assume most people will either have java or wont have a problem if your installer prompts an installation of the JRE.
This used to be true; not so much any more, at least so far as Apple goes. Apple has outright disabled Java on newer releases due to security problems.... or at least, that's the excuse Apple gave. I honestly wouldn't be surprised to see Microsoft follow suit. When you've got the Department of Homeland Security telling people to disable/remove Java, that's all encouragement Microsoft needs... if their lawyers give them the go-ahead that is.
Java is still out there on all platforms, it's just not quite so simple to assume its there as it was even a year ago.