Here are a few of my favorite Model Railroad related websites.
 
New Haven Model Railroads
Bill Chapin's layout in progress.
When he's finished with this layout it will be huge! He's basically modeling the entire western division of the New Haven Railroad. I suppose it should come as no surprise since he's an alumni of Rensselaer Polytechnic.

Jim Fellows' New Haven Railroad in 1956.
At least I think he's modeling the New Haven. He's a regular clinician (and runs the clinics) at the NHRHTA Reunion each year and does great work. At this point I believe he's modeling anything that appeared in New England, but he seems to still lean heavily toward the New Haven.

Peter Ness' New Haven Railroad in 1959.
Peter also helps run the clinics at the NHRHTA Reunion and also does great work...even through his NH 10' IH Postwar Box Car is still missing a few rivets :>)
I've learned a lot from Jim and Peter about modeling the New Haven accurately.

Rob Gross is also modeling the Highland Line during the transition era.
He usually makes it up to the NE Proto Meet (from Florida) each year.

Kathy Millat in the UK is modeling the New Haven as well and has done some spectacular work.

Bill Shanaman has a lot of pictures of his layout, including the Valley Line here. He also a couple of videos on the Model Railroad site.

The Stamford Model Railroad Club is a longtime O-scale club layout founded in 1939(!), with construction of the layout started after WWII in the basement of St. Johns Church in Stamford. 

Other Model Railroads
Bill Schneider's Old Woman in the Back Bedroom (New York, Ontario & Western).
It's an amazing layout in a small space, a lot of fun to operate, and an inspiration for my prior and current layouts. I've actually "known" him for some time, he worked at the hobby store I frequented as a kid, and owned another one I visited when I moved to another part of the state a couple years after I was married...and just before he closed the store. He even recognized me. I finally 'met' him properly at the NE Prototype Meet.

Joe Fugate's Siskiyou Line.
One of the most useful sites I have found. Great information and clinics from Joe. The forum was very active for a while, and browsing through the archives is very worthwhile. Joe is the publisher of Model Railroad Hobbyist, and the forum activity has moved to that site.
 
Tony Thompson's Modeling the SP blog.
Fantastic information, and at a much more consistent pace than my site.
I see more kitbashed tank cars in my future...
 
Craig Bisgeier's Housatonic Railroad.
Craig's modeling the turn of the (last) century model of the Housatonic Railroad. Great layout and great website.

Historical Information - New Britain
Local History Room at the New Britain Public Library
They have a lot of pictures from the last century, corporate records from the various industries, and the city directories. The directories are similar to a modern day phone book (although not everybody listed has a phone), but they also have tenants listed by street. 

I had heard that the society was no more, but it appears they are back. They're also on Facebook.

New Britain Industrial Museum
If you're in New Britain, you can visit the museum on Main Street. This is focused on the industries themselves, and the many New Britain inventions (beginning with the coat hanger).

History and Genealogy Department
At The CT State Library has a large collection of maps and materials as well. They also have online access (from the library only) to the CT Digital Sanborn maps.
 
Historical Information - Railroad
The Alphabet Route
This is a great website that covers prototype and modeling information for the Railroads in this agreement - NKP, W&LE, P&WV, WM, RDG, CNJ, L&HR, NH. The site is growing, but it already includes rosters, diagrams, some documents (consist books, etc.) and other useful information.
 
DOT Investigations of Railroad Accidents 1911-1993
This has reports for all railroads, but you can search for the New Haven. It doesn't have all of them, but there are quite a few.

New Haven Railroad Historical and Technical Association.
The first railroad historical association, and publishers of Shoreliner magazine. The online forum is a must for any fan of the New Haven.

Railroad Archive
At the Dodd Research Center at UCONN. There are some digital archives online, and much more available in Storrs. Well worth the trip.

New Haven Railroad Resources
Compiled by the CT DOT. They also have digital copies of the valuation maps. Contact the compiler listed in the report for copies.
 
Fantastic reference of NYC and subsidiaries freight cars and appropriate models.
 
The definitive list of PRR freight cars and appropriate models.

Steam Era Freight Cars
A site originally started by Ted Culotta of Speedwitch Media, it is currently managed by another. Updates are very infrequent, but the existing material is must read.
Maps
The University of Connecticut Library
Their collection of original New Haven Railroad valuation maps is now available online. These are early maps, from around the 1920's I believe. They are high resolution scans that can be zoomed in to look at all of the details. A great resource.

New Haven Railroad Resources
Compiled by the CT DOT. They also have digital copies of the valuation maps. Contact the compiler listed in the report for copies.

Historical USGS Maps of New England and NY
At the University of New Hampshire Library.

CT Aerial Surveys 1934
Not maps, but they might as well be. These are a great companion to any map.

History and Genealogy Department
At The CT State Library has a large collection of maps and materials as well. These include the physical copies of the aerial surveys above, plus additional years not available online. They also have online access (from the library only) to the CT Digital Sanborn maps.

Bing Maps
While there are several mapping sites on the internet and pretty much all of them offer current aerial views, only Bing Maps provides the Bird's Eye view. This is a fantastic aid, allowing you to view the actual buildings from an angle from above (and quite different from Google Maps Street View). This is particularly helpful to view buildings in areas that aren't easy to visit in person. Trackwork (both existing and the evidence of older tracks) are visible in many areas. In particular, look for the old tracks still embedded (and buried) in the Stanley Works complex. There are quite a few buildings throughout New Britain that are still standing.

Prototype Photo Sites
American Memory at the Library of Congress
There is some great material here, especially the 29-page report and 90 photos of the Fafnir Bearing Plant. There is also a string of photographs of women working for the Railway Express Agency taken at the station in June, 1943.

CT History Online
Lots of historic photos, although they tend to be from the 1930's and earlier.
A great resource for photos of defunct railroads. Most of the photos tend to be from the 60's and later, but it's still very helpful.

New Britain Rephotographic Project
While there is only one picture (North Main Street, looking south in 1950) that is of direct use, there are several other pictures from 1950 that are helpful for general historical info, such as automobiles.

New England Railroad Photo Archive
Lots of photos posted by members. Like the Fallen Flags site they tend to be of later eras, but more early photos (1940's and later) seem to be cropping up.