Yeah, VW does have it's quality issues. I've been rather lucky with mine. One MAF, one O2 sensor, and one temp sensor. None of which left me stranded. Other than that, just routine maintenance which only helps me spend extra time with my car.
Toyota's quality is definitely up there. I just manage to get weird problems with mine. My first Toyota had a bad clutch pedal assembly (known problem, they all had them). Toyota just wouldn't fix it. Had it in about 8 times in 2 years for it. They replaced it twice, greased it many times, and even tried replacing the master and slave cylinder. Dealership often told me it was normal and that even the brand new vehicles had the problem. I finally gave up.
My second Toyota suffers from a rattling seat. It moves on the track, the pivet points to adjust the seat rattle and move. Every Sport Edition 4Runner has the same problem, even right out of the factory. They did finally seem to fix this one (according to the message boards). I also go through brakes quite a bit. First set lasted 17,000 miles. Second set lasted 7,000 miles. The third set got to 2,000 miles before they started squeeling. On this issue, however, I think it's dealer related. They squeel even when I'm not depressing the brakes, think the calipers are sticking.
Other than annoyances, the Toyota goes strong. Never had so much as a valve or sensor to replace. And never worry about being stranded.
The VW, while it has never left me stranded, I sometimes think, "It's gotta happen someday". But, I will say. The Toyota has NEVER put a smile on my face like the Beetle has.
