Webtag: UK Department of Transport Guidance on Modelling and Appraisal.
Design Manual for Roads and Bridges: UK Highways Agency Guidance - Volume 12 is on highway modelling.
Travel Model Improvement Program: US DoT site, follow "resources - clearing house" links to research reports.
Australasian Transport Research Forum: archive of ATRF conference papers. Unfortunately the only useful search key is the author of the paper.
European Transport Conference: archive of ETC conference papers.
Passenger Demand Forecasting Handbook: PDFH is a bible for rail forecasting. It is not free!