Current Timetables
Particularly useful for modern day scenarios, simply pick the area in which you are creating your scenario and you can easily put together the relevant traffic. Here are three but there are more available that do a similar job.
http://www.realtimetrains.co.uk/search/advanced
http://www.opentraintimes.com/
http://www.headcodes.info/
Network Rail also publish the Working Timetable.
http://www.networkrail.co.uk/browseDirectory.aspx?dir=\Timetables\Working%20Timetable%20%28WTT%29&root=\Timetables\Working%20Timetable%20%28WTT%29
Railtours
A very useful site to provide reference for all manner of railtours up and down the country. Often includes information on timings and formations.
http://www.sixbellsjunction.co.uk/
Historic Timetables
http://www.timetableworld.com/index.php - Many historic timetables covering the whole country.
http://www.1s76.com/ - Historic information about CrossCountry services.
http://web.archive.org/web/201206181844 ... ratis.com/ - Site no longer available, but viewable through the archive. The 'Where Were You' section is particularly useful.
http://steverabone.com/Hellifield%20Website/ - Useful for the S&C route.
http://www.bexley-is-bonkers.co.uk/phot ... 2_14.shtml - Network SouthEast timetables.
http://www.michaelclemensrailways.co.uk/?tok=34 - Old Western Region Working Timetables.
http://www.ribblevalleyrail.co.uk/Old%20Timetables.htm - Many old timetables from many areas. Very interesting.
http://www.railtables.co.uk/ - Another fantastic timetable archive.
There are loads more, I just need to dig them out.