I have owned 2 8valves and a VR6.
There is no contest really, the Vr6 feels like a real 'grown up' car, with a wonderful, stacks of performance, but perhaps most importantly an amazing noise. However, the downside is that the V6 noise makes you want to boot it, which in turn leads to dismal MPG's. VR6's also seem significantly more expensive than 4 cylinder models.
Out of the 8v and 16v, I'd go for the 16v everyday - they don't seem to have much premium over 8 valves and cost only a little more to run. As with all cars this age, there are stacks of trashy cars in Autotrader, its a case of sifting through for the good ones. The 16v isn't exactly refined, but it does have stacks of grunt, whereas the 8v is simply the same as a Mondeo / Vectra / Escort 1.8 etc. That said, there is a satisfying 'unburstable' feeling about the 8v unit.
The reason I ended up buying 8 valves both times is because there are many more of them, and also (as they were actually cheap cars in 96-98) there are plenty that have been a housewife's car / retired person hence mint and easy life (the Gti was only a few £100 more than a 1.8 GL - so people bought them that weren't wanting a GTi style car) . Fewer 16 valves to choose from. I've found the local paper to be a great place to pick up both of my 8 valves from middle aged owners who have maintained the cars well.
To sum up, I'd probs go for a late 16v if i was spending up to 3k. If I was spending £4k for a decent VR6, I'd rather chip in an extra grand and get a mk4 gti T. Its also worth noting that tidy early mk 4 125bhps are around £3.5k now