Biodiesel can be used in any diesel without modification, it is a direct replacement for petroleum diesel.  However biodiesel is known to break down natural rubber which is often found in diesel vehicles built before 1992.  The fuel lines in these vehicles can be easily and cheaply replaced.  Biodiesel is caustic and can "clean" the diesel "gunk" that builds up in the fuel tanks of high mileage diesels.  This gunk will then get caught in the fuel filter of the vehicle, therfore you should carry a few extra fuel filters.  If you lose power or the engine just shuts off the fuel should be the first thing that is checked.

Biodiesel has a higher lubricity then ultra-low sulfur diesel which will provide a higher efficiency for your diesel engine.  The ultra-low sulfur diesel fuel has caused problems in older fuel injectors and fuel pumps it cuases leaks due to these parts requiring a certian lubricity to form a seal.  Biodiesel can restore this lubricity even in blends as low as B5.  

Quality issues in the fuel can have a negative effect on the engine as unreated mono, di, and triglycerides, or to much free glycerin can clog fuel injectors and cause harmful buildups on cylinder heads.  If you plan on brewing your own fuel you should run the 3/27 test often to determine if you have achieved a proper reaction.  If the 3/27 test fails then you should rereact your fuel as it is probaly not a good idea to run it in your engine.

You may also find it beneficial to install a fuel tank heater if you live in a cold climate as B100 is known to gel at temperatures below 40F.  If the biodiesel is blended to B20 the gel point is lowered to an estimated -20F.