Having just returned from Kinmen / Jinmen / Quemoy over the 4 days Dragon Boat Festival holiday, here is what my experience was:
Having a German Passport and a Taiwanese ARC, it was no problem for me to get a Chinese Single-Entry visa good for staying 30 days in China from within Taiwan. I just went to a nearby travel agency in Nangang, gave them my passport, 2 passport photos, an ARC copy and a letter of employment from my employer, and 7 days later I got my passport back with the visa. It cost me 2700 NT$, but for some reason for US citizens it would have cost ~9000 NT$. They sent the passport to Hong Kong, and the visa was given there.
For going to Xiamen / Amoy, you just go to the port located to the south-west of the main Kinmen island, buy a single way ticket (~600NT$), and go on the boat. It seems there are no return tickets. Don’t forget to exchange some NT$ to Yuan (PRC Money) in the main port hall, since on the chinese side port in Xiamen there is no way to exchange anything, and the taxis there only take Yuan. Also to buy the return ticket from Xiamen to Kinmen you will need to pay with Yuan (~160 Yuan), so either take enough with you from Kinmen, or exchange / get from an ATM in downtown Xiamen.
After you arrive in Xiamen you have to fill out a yellow entry/exit form, and with that go through immigration/customs. Additionally, on the boat, I had to fill out a questionaire about where I have been the last time, and if I show any signs of flu. I guess that’s a swine flu thing, though, as well as the PRC officials scanning everyone’s temperature.
Outside the taxi drivers will try to rip you off, quoting ~20 Yuan to go to the ecntral street there, while when you insist on using the taxameter it will be ~10 Yuan. For 10 Yuan they will offer to get you to “downtown”, which is a pretty boring area nearby, where you probably don’t want to go.
It seems you can not take your car/scooter on this boat by the way. There seem to be more than just this one ship that you can take, at least on Xiamen side ther were several ports where you can get boats to Kinmen -
Just FYI (or for your Taiwanese friends): If you happen to be a Taiwanese citizen (from anywhere, not just Kinmen), all you need to go to Xiamen is your Taiwanese Passport. The procedure is a bit more complicated, though. You will need to get a special PRC passport for Taiwanese at the Xiamen port, before you can exit customs. For this you have to provide a passport photo (can also be made there, costs ~30 Yuan, and takes only a few minutes), that you ahve to glue to a special form that you also get there. With this you will get a light green “passport”, saying something like “Resident of Taiwan going back and forth to China passport”. It costs 150 Yuan, and they don’t take credit cards or NT$. So make sure you bring enough Yuan with you…
The way back is easy for Taiwanese, they can just pass the taiwanese immigration/customs. For me it additionally involved filling out an immigration form, but that’s it.