I did several side-by-sides when old Velvia 50 looked like it was being discontinued for good. There were many situations where differences were minor and many where they were night and day. For any shots with a lot of green (i.e., summer forests, which I shoot a lot of), I preferred 100F's yellower palette to 100's bluer palette. For general shooting, 100F gave nice saturated colors while 100 sometimes went over the top. For sunsets and sky colors, it all depended on the actual intensity - a vivid red sunset looked great on Velvia 100F and too red on 100, but a more muted one looked duller than reality on 100F and more natural on 100. Brown leaves and tree trunks often went too red on 100. Fall colors could be muddy on 100F. Caucasian skin tones were better on 100F. Twilight and moonlit landscapes looked better on 100. In general 100F held better shadow and highlight detail than 100, but neither was as good as 50.
In the end I decided I'd have to just shoot both, switching between situations, to get the most pleasing results, when lo and behold Fuji announced Velvia 50 was coming back. I about danced in the streets because I agree that 50 really is the gold standard, with the richest blacks, smoothest contrast, sharpest edges, and most pleasing color of all the Velvias. When I need 100 speed I sometimes prefer pushing it rather than going to one of the 100-speeds, after comparing all three. I have found uses for the 100 speeds (100 is great for moonlit landscapes, 100F is good for green forests when 50 is too slow, 100F pushed to 200 looks great in muted light, etc.), but I go with 50 probably 95% of the time.
Of course this is just my preference and you'll have to do your own tests - just don't let anyone tell you the Velvias are all the same.