There's obviously a difference in sound so I'll just skip that. The Type S has - not sure how to express this - a more "precise" feel than the regular HHKB. And depending on how new it is, sometimes you can feel the silencing rings sliding in the switch housing, which is the source of the "scratchy" feeling some people complain of.
The Type S has a typing feel, IMO, very similar to a Realforce, where the regular HHKB feels like no other Topre board.
For the record, I own a Realforce 87UB55, a HHKB, and I'm typing this on my Hasu'd Type S.