In short, Cubase is a producer's tool for audio/MIDI music creation while Nuendo is a complete media production system capable of handling many tasks such as audio-for-video post production, dolby 5.1 and DTS encoding, and stereo mastering, among others.
Nuendo's strength is in its versatility while Cubase shines as a dedicated music creation tool.
While there is essentially only one flavor of Nuendo, there are several incarnations of Cubase:
Cubase VST/32 5.1 is the most popular and powerful edition in the old Cubase line, now being supplanted by Cubase SX.
Cubase SX is the new flagship program from Steinberg. Essentially, it is Cubase 5.1 rebuilt with Nuendo technology. It is based on the code from Nuendo. I have had only minimal hands on experience with the program, but it seems to be Cubase 5.1 with a loop editor (stolen from Sonar?); however, I was quite impressed by the program as it does have innumerable little improvements over Cubases 5.1 that really do add up to a distinct advantage over the previous version.
There are two stripped-down versions of Cubase, called
Cubasis VST 3.0 and Cubasis Go! 3.0. These programs are still quite functional and can be had for around $80.00 and $60.00 (USD) respectively.
There are several other native programs out there if you are interested, including Digidesign's Pro Tools Free, Emagic's Logic Audio, and Twelve Tone Systems's Cakewalk Sonar. I have not used Pro Tools, Logic seems a little awkward to me (although Emagic claims that 2/3 of top 10 singles are made with Logic), and Sonar, my favorite program, is very user friendly. Logic and Cakewalk are both available in stripped-down versions.
Hope this helps!
-- David