I would start out with winehq.org first.
Also:
I have installed it on Windows and it works well.
That is not a good comparison. Lol. A lot of people use that as a comparison, but it is actually moot; it was written for Windows, so of course, one would expect it to work on it's native platform. Wine/POL/POM is not Windows, so the comparison is irrelevant. :)
One thing I would look at is that, because it was written for Java, and JRE is native to Linux, you might want to inquire about the source code, and maybe see if it can be ported. If not, I would recommend starting out searching at http://appdb.winehq.org for that program, and see if it is available, and if it works. If it is in that site's listings, you will likely find things to get it to work. If there is no listing, you should file a bug report with WineHQ for that application, as POL/POM is just a GUI for Wine. Although, if you do find out any information and get it working to an acceptable level, let us know, and perhaps someone (or yourself) will write a script to get it working through POL/POM. Check the Wiki for more information on writing scripts.
