Most programs should work with only minor modification. GUI programs will not work. This is intentional, so that people won't load GUI components from a remote system, stupidly expecting them to show up on their own computer.
Currently, there are issues with java.io.File. Sun's version was designed under the assumption that java programs won't be changing their current directory. For relative files (ie "./run.sh", for example) java will always work with the file from the directory that the JVM was loaded from, completely ignoring the "user.dir" system property, even though I patched it to work through an InheritableThreadLocal. The next release will remedy this problem if at all possible. I plan to implement something similiar to JDistro's VFS system (see http://www.jdistro.com). In fact, JDistro is the project that made me realize that it was even possible to replace standard java classes at runtime.
Note: There are two valid user names currently setup: root (password: 'lockout') and guest (no password, just hit enter). The system is also setup to accept new account formation from the "new" user account. Look at the comments in the default system properties file (usr/src/jinx/bin/jinx/defaults/system.properties) to learn how to disable this behavior.