I'm pretty happy with the audio overall in my 98 GS300, the only problem is that the stock woofer is blown. Can I upgrade to an aftermarket amp+woofer without changing anything else?

 

Of course you can. The type of install you are asking about is likely the most common and popular audio upgrade. You can do this a couple of different ways. You will need a woofer, an enclosure, an amp and a run of power wire from you battery. When it comes to the signal, you can either tap the factory sub signal with a LOC (line out converter) which will take you from speaker level connections to RCAs, or you can use an OE integration processor. The LOC is certainly the easiest and likely the best choice for someone just getting started. There are lots of threads on aftermarket sub installs. Do some searching and you will find complete how to instructions.