You can do this by specifying the firefoxDefaultPath in you're eclipse.ini:

For example, if your eclipse.ini looks like the following:

-clean -showsplash com.genuitec.myeclipse.product.ide --launcher.XXMaxPermSize 256m -vm C:\Apps\Jdk1.6.0\bin\javaw.exe -vmargs -Xms512m -Xmx1024m -Duser.language=en  -XX:PermSize=256M -XX:MaxPermSize=512M

Then you need to add it like this:

-clean -showsplash com.genuitec.myeclipse.product.ide --launcher.XXMaxPermSize 256m -vm C:\Apps\Jdk1.6.0\bin\javaw.exe -vmargs -Xms512m -Xmx1024m -Duser.language=en -DfirefoxDefaultPath="C:\Program Files\Mozilla Firefox\" -XX:PermSize=256M -XX:MaxPermSize=512M