We finally have some hard answers on the popular vote.
According to Real Clear Politics, Hillary Clinton won the popular vote if you give zero votes to Obama in Michigan and/or you leave out estimates for the four caucus states that have not released popular vote totals (IA, NV, ME, WA).
However, if you use estimates for those four states and you give Obama the "uncommitted" vote in Michigan the final tally was:
That's 48.1 percent to 47.9 percent. Obama's margin of victory was thinner than turnip soup, as Dan Rather would say.
Also, Open Left has a good rundown of when each candidate earned their delegates. (Obama pulled down more than Clinton in January and in February, there was essentially no difference in March, and Clinton beat Obama in April-June.) Noting that the only period where the results were truly lopsided was that post-Super Tuesday period in February, blogger tremayne notes:
Delegate-wise, Sen. Obama won the race by essentially tying Sen. Clinton on Super Duper Tuesday (can we go back to just regular-sized Super Tuesdays or smaller?) and then going on his "rest of Feb. run." 121 of his 126 pledged delegate margin occurred in this period. And incidentally, only 4 of those 11 contests were caucuses which benefited Obama by a margin of +48. The other +73 pledged delegates in this period came from primary states.
For an excellent article on how Obama's people understood the rules of the race and the impact of the calendar from the very beginning, check this out.