I searched and it seems like its been a while that we have had a topic on this subject.
Remember the old 100 link per page limit? I am probably old fashioned, but have always tried to adhere to that one. I have built lots of vertical silos (with some cross-linking). Obvious drawback here is lots of clicks for the user, but the benefit is a nice themed path to the destination page - think good scenery along the way.
Just checked target and walmart - both have >1,000 links off of their home page. We can't all afford the usability testing that they probably do, but, you've got to figure they probably don't have it all wrong.
One of the old time issues used to be the navigability of the links for spiders - with dhtml or java flyouts etc. - but, googlebot seems to chew through just about anything these days. So, no issue there?
Then there was PR sculpting/efficiency. But that is a zero sum game anyway, no?
I am about to pull the trigger on one of my sites. Curious about other views and experiences.