I did this project about 1.5 years ago and have been very happy with the results. There is a ton on the forums about this, but I think I can contribute a few tips:

Material - I thought about using glass, but didn't like the idea of glass on a boat (prolly more worry than actual problem). Also, I wanted to be able to remove old and install new ports at the same time (w/o a trip to the glass cutter). As David mentioned, there is a lot out there about water/salt/UV turning Lexan cloudy. However, one particular product MR10 Lexan by GE is coated to resist this, and even West sells it for use in boat ports:

http://www.westmarine.com/1/1/9643-smoked-lexan-mr10-hatch-lens-replacement-from-ge.html

I found it very easy to work with (table saw for rough, trim with a jigsaw). Also, you can buy scraps of it for pretty cheap on eBay, which is where I got mine:

http://shop.ebay.com/i.html?_nkw=mr....m270.l1313&_odkw=mr10&_osacat=0

Cutting Windows - I read somewhere on the forum that the holes are not exactly the same sizes, and that some users had to cut each from the previous port to get the sizing right. I went to great lengths to do this on my boat, which is 4 hours away, only to eventually find that all my new ports were essentially the exact same size and were interchangeable. Would have saved me a huge amount of time to cut them all at once. Maybe your boat is different...

Caulk - I used GE Silicon II, white. I used a ton of masking tape on both sides of a caulk line so I could smooth it to the tape with my thumb, then remove the tape. The results looked like a brand new boat. The silicon needs a bit of special attention to get dirt off when I scrub the decks, but its not that bad. I also figure the silicon will be very easy to remove and redo when the time is right. I believe there was a post about this taping method somewhere...

Hope this helps.