I, too replaced the Plexi ports with tinted (grey) auto safety glass last Spring. I used black sealant inside and out, with masking tape, etc. It took a couple tries on the first piece to get it looking right. Attached is an exterior shot -- I don't seem to have an interior one.
Harley's windows look great. Not as great as Dave's trimmer, but great nonetheless.
If you're simply looking to replace the ports as they were originally installed, though, I recommend a high quality plexiglass (acrylic). I know that many people use lexan, and I have in the past, but it has some limitations.
The biggest is that lexan scratches very, very easily. It is stronger than acrylic, but is more susceptible to scratching. Also, it's about 4x the cost and is more difficult to cut than acrylic. Another challenge, at least here locally, is that it's difficult to find a retailer that will sell it in a size other than a full sheet.
Acrylic's biggest limitation is that it is prone to yellowing. However, newer, high-quality acrylics have all but eliminated that issue. It's also affordable - I replaced my ports for about $20. Finally, it's very workable - it cut easily, quickly and precisely with a quality jigsaw blade.
Auto safety glass is also a reasonable option - it wont yellow or scratch - but it is a bit more expensive, particularly given that you will generally have to pay to have a pro cut the windows. I think I was quoted about $80 for all four windows by the same guy that did them for Zephyr.
Jason - great writeup on your site. I think that when I do this, I will go the auto glass route. The incremental cost is not too bad when compared with other boat expenses, and it looks like they will last forever unscratched.