I've owned both of those cameras, as well as the Pentax PZ1p and the Nikon N90s.
The best camera of the four is the Nikon F100. No contest. Unfortunately it does not take Pentax K-mount lenses. That's a huge drawback for me, as I primarily shoot Pentax.
The Pentax PZ1p is directly comparable to the N90s. It's not comparable to the F100 or the MZ-S. The PZ1p and N90s are huge, ugly, plastic beasts that work very well. I actually give the edge to the PZ1p over the N90s, because Pentax adopted dual control wheels and the N90s is crippled with only one. But AF is crude on both cameras and you definitely feel like you are shooting a product designed in a previous generation.
The MZ-S is the closest that Pentax ever got to something like the F100. Had Pentax released the prototype MZ-1, I suspect it would have been the equal to the F100. But the MZ-S is something completely different than the F100.
First, the MZ-S is light. It feels like half the camera of the F100. But build quality is similar -- true metal alloy body, combined with a plastic film door (to the dismay of both cameras' owners.) Autofocus performance goes to the F100, which is screaming fast and also supports newer protocols like AF-S and VR lenses. The MZ-S autofocus is perfectly satisfactory, especially in good light. But it's not up to the Nikon standard. (Pentax lost ground here from the PZ1p, which held its own against the N90s.) For flash usage, both are very good -- though Nikon's flashes themselves are generally superior to Pentax. The MZ-S will use the latest flash technology (P-TTL) and was introduced alongside the still-current AF360FG flash. For the F100, you will want to use a last-generation flash like the SB26 or SB28 (i.e. regular TTL.) The battery situation for the MZ-S is tricky. I prefer the MZ-S without the grip, but then you have to use expensive little lithium cells. With the grip, you can use AA batteries. I think Nikon had it right using AAs in the plain F100.
While in general I think the F100 has the edge, you come back to lenses. I love Pentax lenses, and even the famed Limited lenses are a bargain. The best, most modern camera to use Pentax lenses is the MZ-S. The combination of an MZ-S and Limited lenses is unlike anything else in the camera world -- small, light, sturdy, reasonably high performance. It's kind of like comparing a Mazda Miata to a Corvette. The Miata will never be as quick as the Corvette, or feel as substantial. But it will deliver a special experience that might be worth forgoing brute strength and speed.