The Gilder Lehrman Institute of American History's quarterly online journal put together a fantastic issue on nineteenth century technology a few years ago. There's an essay, called "Transcontinental Railroads: Compressing Time and Space," by the historian Richard White that provides a great introduction to thinking about the railroad and its significance for American society and culture. There is also a link to a page of additional resources with a solid bibliography and some interesting links.
The same web journal did an issue on the American West that provides a broader historical context in which to understand the significance of the railroad. The five, short thematic essays are all worth reading for those interested in a little more perspective.
The Central Pacific Railroad Photographic Museum maintains a page with an absolutely mind-boggling amount of information. Sifting through some of their online offerings is well worth the time. There are loads of great photos, links to primary source documents, timelines, and answers to just about any question you could think to ask about the transcontinental line.
One of the best organized and most helpful sites on the subject is the companion website to the PBS American Experience series documentary The Transcontinental Railroad. The site includes not only a full transcript of the program, but also pages and pages of supporting information and essays, all well-researched but easily digested. Pay particular interest to the "People & Events" and "Special Features" links. James Surowiecki's article comparing Doc Durant's big scheme to the Enron scandal provides a wonderful way to approach the issue.
American Memory has a very cool interactive railroad maps collection. See the West as the surveyors sketched it and as it came together in the minds of those who mapped it first. The site includes a useful tutorial for working with the collection.
The Union Pacific's corporate web page has a link to history and photos that hosts information from the UP museum.