I had a '93 Polo Green II ZR-1 for 5 years. They only made 448 cars each year from 93-95 (405 h/p cars), only 20 in my color for '93. It was hands down, the best Vette I had to-date.
So, to answer your question, the ZR-1 will always be much rarer than the Z06. I sold my 30k mile car for the mid thirties late last summer - original sticker was close to 70k /phpBB/images/smiles/icon_eek.gif ! Of course many ZR-1's sold for less than MSRP once the initial furor died down. From my observations, the only ZR-1's that are holding most of their original value are extremely low mileage garage queens which can have their own problems since they have sat unused for years.
Truth is, while the ZR-1 was awesome in its time, and will always be a very special car in the pantheon of Corvettes, it was a flawed vehicle. Build quality was very spotty, chassis was weak (car would torque noticeably on a high speed banked track), car had substantial understeer due to about 200 lbs extra weight over front wheels... that car was a heavy mutha!
Engine was a work of art, but very few people could or would work on it. Scarcity and expense of parts is becoming more and more of an issue. Push rod engines are not as exotic, sexy, and sophisticated, but they are also not as expensive to mod or repair while making similar power.
I didn't want an exotic, I want a kick-ass affordable, special car that can just about outhandle and accelerate anything up to cars costing 50% more.