If Java runs properly the IDE may work. For programming using normal COM ports, you'll need to get a RS232/TTL adapter. These are cheap and Google leads the way.
But let me ask you, why still use Win9x ? You do realize that there haven't been any security fixes for this piece of software for more than 2 years! Going online with software in such a state is part of the whole spam/virus/bot/worm problem we all face (or don't when making the right choice).