Here's a fascinating article on some of the major problems with our nation's primary voting process, along with some possible solutions. I'm a huge fan of Instant Runoff Voting and think it's a travesty that it isn't in use today.
Consider the Republican contest this year. John McCain earned his frontrunner status in January without ever winning more than 37% of the vote in a primary or caucus. The Republican's winner-take-all rules also aided him in gaining frontrunner status. Even on February 5th, where he essentially locked up the nomination, he only won a majority of the vote in three states. Whether Sen. McCain is the right nominee for the Republican Party is not the point; the reality is that he easily could have been a splinter candidate who didn't reflect the views of the majority of Republican voters.
On the Democratic side, even with proportional allocation rules mitigating the impact on distortions in allocating delegates due to plurality voting rules, the lack of instant runoff voting had a clear impact on the race. The media inevitably focuses on who wins the most votes, no matter how low that percentage might be - consider New Hampshire this year, where Sen. Clinton won a big boost despite securing less than 40% of the vote and potentially not being able to have defeated Barack Obama if supporters of the remaining candidates could have indicated a second choice between the frontrunners.