Kidding man, I'm not sure what the actual differences are in the shafts besides size and weight, but the 4" shafts have been known to cause rubbing issues if your car is lowered substantially, as in around 2 inches or so. I've got a 4" one that has worked great for me. I'm lowered about an inch and have no clearance issues what so ever. Mine weighs in around 18 pounds, I think the 3" ones weigh in at around 16 pounds.
When they first started coming out, the 4" shafts were the only one's available as far as I know. Since others have started making them, they've made them in smaller sizes.
That's all I'm aware of, but maybe some others will chime in with other differences.
Cool so where are some websites I can get pricing. I have done a search and seen people talking about power house and jpc but I cant find any info on them. The only ones I have actually found info on are the apd's & driveshaft.com. Where else can I look to for this info?
http://www.tillmanspeed.com/ sells a 3.5" one, I believe it's the Denny's driveshaft, he had a group buy on it on another website. There have been several occurences of people having some vibration issues with the flange they supplied for this one, but Denny redesigned the shaft so that should be gone, from what I read.
The first 2 sites are being redesigned/worked on, so you might have to call them. CR at Tillman and I think it's Joe at Powerhouse are both very helpful over the phone and will tell you everything you need to know. Powerhouse will let you get to the site, but when you look at products, nothing shows up. He knows about it and it working on it from what I've been told. Tillman is just redesigning theirs.