An article by Brian Stetler in the October 30th New York Times titled "Following the Script: Obama, McCain and ‘The West Wing'" provides a great look at a number of the parallels. The opening paragraph says,
Parallels between the final two seasons of “The West Wing,” which ended its run in May 2006, and the current political season are unmistakable.
Wikipedia has a good summary as well.
Similarities between the fictional 2006 election and the real-life 2008 U.S. presidential election have been noted in the media: young minority Democratic candidate (Matthew Santos on the show, Barack Obama in real life) has a grueling but successful primary campaign against a more experienced candidate (Bob Russell on the show, Hillary Clinton in real life) and chooses an experienced Washington insider as his running mate (Leo McGarry on the show, Joe Biden in real life), whereas the Republican contest is determined early in the primary season with an aging maverick senator of a Western state being the nominee (Arnold Vinick on the show, John McCain in real life) and then a socially conservative running mate from a small Republican state (West Virginia Governor Ray Sullivan on the show, Alaska Governor Sarah Palin in real life).
Writer Eli Attie called David Axelrod to talk about Obama after Obama's 2004 Democratic National Convention speech and says that he "drew inspiration from [Obama] in drawing [the Santos] character," while actor Jimmy Smits says that Obama "was one of the people that I looked to draw upon." Writer and producer Lawrence O'Donnell says that he partly modeled Vinick after McCain. Obama's Chief of Staff, Rahm Emanuel, is said to be the basis of the Josh Lyman character, who became Santos' Chief of Staff.
Other perceived similarities include Santos being "a coalition-building Congressional newcomer who feels frustrated by the polarization of Washington," Santos delivering "a speech on race at a critical moment for his campaign" (a parallel to Obama's A More Perfect Union speech), Santos and Obama both being Bob Dylan fans, Vinick being criticized as "not conservative enough," etc.
In addition to the above parallels, I know of at least one more. Although I cannot find a reference to this anywhere on the web, Hilary Clinton's selection to be the next Secretary of State parallels Matt Santos offering the job to his opponent, Arnold Vinick (Alan Alda). Sure, Vinick was Santos' Republican opponent in the November election but offering the job to a chief rival - of either party - is another weird parallel.
And with the newly developing situation in Mumbai, India, I can't help but wonder if we'll see a parallel with the fictional incident in Kazakhstan on The West Wing.
If you get a chance to watch the past couple of seasons of The West Wing, I guarantee it'll leave you feeling spooky!