Here are a collection of links that I've found to be particularly useful:

MidiShare

Midishare is “a real-time multi-tasking MIDI operating system specially devised for the development of musical applications” that was developed at the GRAME music research centre in Lyons, France. It’s very easy to use and is available for a range of platforms.

Maximum MIDI

Maximum MIDI is a flexible toolkit of C and C++ routines for Windows 95. The toolkit is accompanied by an excellent book about all aspects of MIDI on the Windows platform.

PortAudio

PortAudio is a library that provides streaming audio input and output. It is a cross-platform API (Application Programming Interface) that works on several platforms including Windows and Macintosh.

Cakewalk

Cakewalk are the developers of "Sonar", one of the first MIDI sequencers to adopt the OPT standard.

Cycling '74

Developers of the incredible "Pluggo" set of VST plug-ins. One of the best and most affordable ways to mangle sound that I know of.

CS1x Edit

The one and only CS1x Performance Editor. A vital tool for all CS1x users and an ideal partner to my own CS1x Background Edit.

Sound On Sound

Without doubt the leading music technology magazine going around. The website also has an incredible database. If you're thinking buying any gear then this should be your first research stop.

Robot Software

Robot Software produce a really interesting range of MIDI shareware for the Macintosh. My favourite is Random Music Machine.

The CS1x Archive

Probably the leading place for all things related to the Yamaha CS1x. Unfortunately, doesn't appear to have had any activity for a while.

Linplug

Peter Linsener has developed some great VST Instruments (I may be biased however, because I've helped him write some of the manuals!).

Synthesis Toolkit

The Synthesis ToolKit in C++ (STK) is a set of audio signal processing and synthesis classes and algorithms written in C++. You can use these classes to create programs that make sounds with a variety of synthesis techniques. The ToolKit is extremely portable.

CSounds

In my opinion, this is the best site for all things related to CSound. Created in 1985 by Barry Vercoe, CSound is one of the most widely used software sound synthesis systems. It's extremely powerful, basically letting you do anything you can think of. However, creating music with CSound is more like "programming" and can take a good deal of time and effort to become good at.

Native Instruments

Native Instruments produce a great range of softsynths including the FM7, the Pro52 and the amazing Reaktor.

Noah

No this isn't a link to the site of the famous boat-builder, it's actually a new hardware synth that generates sound using flexible algorithms. If it lives up to the hype it should be awesome!

Neuron

Don't know a lot about this one other than it creates sound using "intelligent analysis and synthesis based on neural networks". It looks interesting although it's very expensive.