Well, a 180mm/F4 would certainly be much cheaper than a 180mm/F1.8 (given
similar quality). Of course you didn't tell _which_ lenses you are talking
about, so we can't guess if that's a possible explanation.

jue

Each MF version has a better feel when focusing manually.  I'm told
that there are a people who also prefer the metal construction
of the AI-s lenses; you wouldn't know anyone like that, would you :-)?

Still, those prices for the MF versions are wildly optimistic.  B&H
still lists both new 20mm f/2.8 AI-s and new 180mm f/2.8 AI-s lenses
at $509 and $729 respectively.  I doubt they sell very many.  On
eBay, the manual focus lenses consistently sell for less than their
AF counterparts.

The 20mm f/2.8 AI-s has the same optical formula as the current 20mm
f/2.8D.  While some people prefer the older Nikon MF 20mm f/3.5 or
even f/4, even in pristine condition the older lenses tend to sell for
less than the f/2.8.

The manual focus 180mm f/2.8 is more of a mixed case.  The AI-s
has a different optical formula which, at least in theory, results
in better T-numbers and slightly less flare.  It's also not an IF
design.  Unlike the AF version, focal length doesn't change with
focal distance, but it's slightly less convenient to use, especially
when using filters.

The first AF 180mm had an ugly shiny black barrel and an awful
manual focusing ringlet; its value in the used market has
suffered accordingly.

Some of these older lenses have a signature character about them that has
been lost with some of the modern lenses that produce perfect and clinically
sterile images.  This is why a lot of older lenses are aggressively sought
after.  This is why many Canon shooters by old Nikkors and now with the
introduction of the D3 you can expect a very sharp spike in the AI lens
arena.

Rita

Old MF AI(s)lenses are, in my opinion, the best lens-line ever made by
Nikon. All glass and metal, an yes, I prefer metal than plasticy modern
brands, even when some of the new ones have been optically improved. In
terms of construction quelity, I think there is no comparison between
those lenses made from the last 70's till now, denominated as AI or AI-s
in the last series. That is the reason why MF lenses are usally much
more expensive than AF ones with similar focal distance and max.
aperture when bought as brand new.
On the other hand, used MF AI(s)lenses are priced lower than actual AF
only because nowadays there is a larger demand on new AF ones because
the AF lenses can be mounted with all their functions on the newest slr
digital cameras (AF, automatic light metering, etc), but not based on
their construction and operation quality. Just try to focus manually one
and the other and make up your choice. Technology goes on growing, not
always producing better products, but always reducing production costs.