I program regularly in R in a professional context, and I write packages for clients or co-workers as well. Some of the programmers here have a Java background and insist on
S4 classes play a strong part in spatial statistics (sensu package sp), where converting from one type of data to the other seems seamless. The pitfall of this is debugging, which has been, in my experience, tedious at best.
So far, I have managed with S3 but may consider using S4 in the future.
With time, as things get played around a lot, I believe they will play a strong role in at least core features of various fields of R (may that be spatial analysis, econometrics, environmetrics...)