I have found the following web sites to be particularly interesting and useful:

  The Bytown Railway Society - Ottawa
    Index to Branchline
The Canada Atlantic Railway Research Site by Rene Gourley
Railways of Eastern Ontario  - this contains accounts, in particular, of the Brockville, Westport and Sault Ste. Marie, the Bytown and Prescott and Brockville and Ottawa Railways.
The Cornwall Street Railway Light & Power Co.
Ottawa Valley Associated Railroaders
Ottawa Valley HOTRAK
Ottawa Valley Garden Railway Society
New York Central's Ottawa Division
Southern Ontario Railway Map Project
Brockville Railway Tunnel
Outaouais' Forest History  (In particular http://www.histoireforestiereoutaouais.ca/en/c24/ and http://www.histoireforestiereoutaouais.ca/en/c16/ )
Perth and District Historical Society   (In particular History of Perth Station by Eugene Kirkham  http://www.perthhs.org/documents/perth-railway-station.pdf
OTrain Fans https://otrain.railfans.ca/  Interactive map including planned extensions. https://otrain.railfans.ca/system-map
Ontario Railway Stations by Rob Hughes

 Altitudes in the Dominion of Canada 1915   A good source for railway and station locations This list altitudes, primarily along existing railways, showing stations, watercourses etc., and mileages.
1901 edition https://archive.org/details/altitudesindomi00canagoog/mode/2up
1915 edition https://upload.wikimedia.org/wikipedia/commons/c/c8/Altitudes_in_the_dominion_of_Canada_(IA_altitudesindomi00whit).pdf
Ontario Land Registry Access  http://help.onland.ca/en/onland-is-here/
CNR in Ontario,  source of CNR and constituent company timetables -  http://www.cnr-in-ontario.com/     
Ontario Geneological Socitey Collections   http://vitacollections.ca/  collections from Ontario libraries, archives, museums, historical societies, community groups and government ministries. Good for Kingston British Whig newspaper.
  Canadian National Railways Synoptical History 1960
 Canadian Pacific list of designating numbers of stations 1 March 1966
  Statutory History of the Steam and Electric Railways of Canada 1836-1937 by Robert Dorman, Department of Transport 1939
Digitized by Google Books https://1drv.ms/b/s!AtV76TBeh9q9gZl77j0WdTxC_fSXlA
The maps, dated 1941, which were published later can be found at http://churcher.crcml.org/Map/Maps1941.html
  Statutory History of Railways in Canada 1836-1986 by Robert Dorman/D.E. Stoltz
  Clippings from the Train Stations in Carleton Place https://lindaseccaspina.wordpress.com/2018/05/03/clippings-from-the-train-stations-in-carleton-place/
  Bibliographical list of references to Canadian Railways 1829-1938 (Dominion Bureau of Statistics)
http://publications.gc.ca/site/archivee-archived.html?url=http://publications.gc.ca/collections/collection_2018/statcan/CS52-D-50-1938-eng.pdf
  Rise and fall of railway building in Ontario from the mid-1800s, University of Guelph 1992  https://archive.org/details/railwaylifecycle00bloo 
  Recollections of Bytown: Some Incidents in the History of Bytown by R.W.Scott Kt. https://www.canadiana.ca/view/oocihm.76366/1?r=0&s=1
This contains background information on the Bytown and Prescott Railway (page 1) and the Canada central Railway (page10)
  Department of Railways and Canals Reports from 1867 etc https://archive.org/search?query=creator%3A%22Canada.+Dept.+of+Railways+and+Canals%22
  Railway Legislation of the Dominion of Canada from 1867 to 1905 inclusive Canada Department of Railways and Canals, Board of Railway Commissioners https://archive.org/details/railwaylegislati00curr/mode/2up
  RaiIway Statistics of Canada and Poor's Manual of Railroads prepared by Andrew Jeanes
  Railway Age (Gazette) USA https://archive.org/details/pub_railway-age

NEWSPAPERS  

 Digital Kingston  http://www.digitalkingston.ca/historic-newspapers/
 Toronto Public Library  must be a resident of Toronto or work in Toronto
     Toronto Star   https://www.torontopubliclibrary.ca/detail.jsp?Entt=RDMEDB0111&R=EDB0111
     Globe and Mail  https://www.torontopubliclibrary.ca/detail.jsp?Entt=RDMEDB0057&R=EDB0057
 Google Newspapers  https://news.google.com/newspapers
 Paper of Record by subscription  https://paperofrecord.hypernet.ca/default.asp Perth Courier, Bytown Gazette, Ottawa Free Press (1871, 1872, 1874, 1875 and 1881.), Ottawa Times.
 Newspapers.com by subscription.  https://www.newspapers.com/ Ottawa Citizen, Ottawa Journal, Montreal Gazette, National Post (Toronto), Montreal Gazette.
Eastern Ontario Review, Vankleek Hill by subscription http://subscriber.pagesuite-professional.co.uk/subscribe.aspx?t=2135&eid=931fff80-a995-43ce-9932-e50072528395
The Almonte Gazette - On Line  https://mvtm.ca/mvt2/the-almonte-gazette/
The Arnprior and McNab/Braeside Archives has a collection of newspapers 1865 to 1937 digitized and available at:
https://search.adarchives.org/findingaid/newspapers 
Stormont, Dundas and Glengarry County Archives - New site with expanded newspaper coverage  https://archive.sdgcounties.ca/index.php/
Newspapers covered - Chesterville Record. The Chieftain, Dundas County Herald and St.Lawrence Reporter, Glengarry News, Iroquois Post. Iroquois Post and matilda Advocate, Morrisburg Banner, Morrisburg Courier, Morrisburg Leader. Mountain herald. St. Lawrence News, Williamsburg Times, Winchester Press.
The Quebec Provincial Archives at https://numerique.banq.qc.ca have a number of newspapers available digitally including the Shawville Equity
 New York State Historic Newspapers https://nyshistoricnewspapers.org/ Free
Issues of old railroad and railway periodicals on-line

MAPS AND AERIAL PHOTOS

 Quebec Topographic Maps and Insurance Plans  http://www.banq.qc.ca enter "cartes topographiques" in the Search (Chercher) window to search for topographic maps of Quebec and neighbouring parts of Ontario, or enter "insurance plans" to search insurance plans for towns in Quebec. You can choose to filter for just those available online in a box on right once the entries come up.
Ontario Topographic Maps - The Ontario College and University Library topographic map collection is a good historical collection covering most of the province from the early 1900s to 1970s at 1:50000.  It is searchable by map sheet name and map number. There is also a tool to convert a location to a map reference to find the correct sheet. Ottawa is fairly well covered. https://ocul.on.ca/topomaps/collection/
Historical County Atlases of Ontario, mainly from around 1879 - https://digital.library.mcgill.ca/countyatlas/searchmapframes.php
 Aerial photos of Ottawa - Ottawa University  https://gsg.uottawa.ca/geo/airphotos
 Scanned Air Photos - 1930-1945 finding aid https://ssimpkin.carto.com/viz/126c8e26-17a5-11e6-907b-0e5db1731f59/embed_map
 GeoOttawa with aerial map layers dating back to 1928 -  http://maps.ottawa.ca/geoottawa/  
 Ottawa Electric Railway, Ottawa Transportation Commission and OC Transpo route maps from 1929. MacOdrum Library, Carleton University
   https://library.carleton.ca/find/gis/geospatial-data/oc-transpo-transit-routes      

MUSEUMS

 Railway Museum of Eastern Ontario  - Smiths Falls  http://rmeo.org/
Railway Heritage Park, Sharbot Lake  Material on the Kingston & Pembroke and Ontario & Quebec railways in the Sharbot Lake area  https://kickandpushca.wordpress.com/
Steve Merediths Railway History Pages provide a wealth of information and links as follows
- Dominion Atlantic Railway https://dardpi.ca/
- Halifax and Southwestern Railway  https://hswdpi.ca/
- Northern Alberta Railways https://nardpi.ca/
- Nova Scotia History Digital Presentation Initiative https://nshdpi.ca/

RAILWAYS IN CANADA

The C. Robert Craig Memorial Library  located in Ottawa, contains a great deal of information relating to Canadian Railways.
   To log into the Library catalogue https://www.crcml.org/library/login.php
The Carillon & Grenville Railway Canada’s Last Broad Gauge by Jim Sandilands
Railway Association of Canada
Old Time Trains – an excellent resource with lots of information on Canadian Railway History.
CNR Ontario Research  a good source for information on CN railway stations in Ontario
Passenger Train Travels of Peter Dawes. 
 Charles Cooper's Railway Pages  including Railway Gauges in Ontario
Steve Merediths Railway History Pages provide a wealth of information and links as follows
- Dominion Atlantic Railway https://dardpi.ca/
- Halifax and Southwestern Railway  https://hswdpi.ca/
- Northern Alberta Railways https://nardpi.ca/
- Nova Scotia History Digital Presentation Initiative https://nshdpi.ca/
Nicola Delja's Youtube video channel has a great amount of interesting video material, much of it from the Ottawa area.  Retro Rail Media

David Hills fascinating description about Sulzer locomotives in Bolivia
Climax Locomotives
Shay Locomotives
Geared Steam Locomotive Works
Railroads of Central America - Jan Pesula's interesting pages on railways in Guatemala, Honduras and El Salvador.