In 2004, the NEHGS asked me to write a series of online articles on passenger lists for their website. The articles are still there and can be read if you are a member. Most people don't care about the background of passenger lists, they are just concerned with the lists themselves. Although the last date on this web site is November 2007, I found it is a good quick site to check on passenger lists* to New England (and Virginia) in the 1600s. It is called Pilgrim Ships.
**There are no such things as passenger lists for the 17th century in New England. These lists are compilations of names from various sources: diaries, letters, writings, licenses to leave England, etc. Many older genealogies placed people on ships much earlier than they probably arrived. It was a cachet to be as close to the Mayflower.
The Mayflower has no passenger list either. We know about the passengers from William Bradford's writings 30 years after the fact (his famous Mayflower Increasings). To date, no other piece of evidence has been found to contradict his memory, which I find incredible. However, he was cryptic and there are several mysteries that have yet to be solved as well.