You can trim the Java fern plantlets from the leaves and plant them once they get any appreciable size to them.
If you have a large tank (>30g, generally), you should consider pressurized CO2. See
http://www.rexgrigg.com/index.html for details, and for nicely priced dry ferts.
For smaller tanks, DIY CO2 via a yeast/sugar fermenter works nicely as long as you have some method of encouraging the CO2 bubbles to dissolve in the water. There's plenty of info on these setups here, at APC, at AC and other places ("yeast method" and "DIY CO2" make good search terms).
For really small tanks, or if you have perpetual $ to burn and a phobia of yeast, there's Seachem Excel. It is not CO2, but it's useful to most aquarium plants (not so much for some mosses, however).
Seachem and others also make aquarium fertilizers (Flourish etc.). They generally come as 2 or 3 bottle systems - to keep iron from reacting w/ other trace elements and/or to keep Ca or Mg suspensions from clouding up otherwise clear solutions. They're pricey, but there are 2 popular DIY schools of thought that are cheap, effective and highly popular:
PPS and EI
For details, check
aquaticplantcentral
^Also has a nice "Fertilator" applet that you can use to figure out how to make your own liquid mixtures or setup dry dosing regimens for tanks of any size.
PS - Got Lighting?