My favorite is the 85 VMax that I still own (owned and sold several other years, but the 85 stays!), the most scary Yamaha I've owned is an 02 R1....with a front brake lever that failed on me at speed!
My best performing Yamaha mx bike has been the 99 YZ250. I've owned several others since then, but I had the best results racing that one/that year.
I have the 09 VMax coming in, and am a bit excited for that!