First a report from the ground by my colleague Evelyn Farkas:

The Flash Point Blog » Blog Archive » Afghan Election Day – and After: Rocks Under the Rice?

Looks like by and large the Afghan elections are free of major problems.
….
The question mark is turnout – an issue complicated by the lack of a voter registration list…
….
One thing is clear — putting the Afghan government fully in charge of these second round of presidential elections and provincial council elections should have been tempered by more international involvement.
….
The international community might have built upon the work it had done in 2004-2005 running the last round of elections and helped the Afghans avoid some of these problems.   This lesson must be retained in order to ensure that the 2010 National Assembly elections — which could eventually be more significant than the presidential and provincial council elections — are administered to a higher standard. 

Those are just some of the highlight.  Read the whole post as well as her other reports from the field:
Live from “Jay-Bad”
Afghan Election Prelude — The Taliban: “…They put him though a wheat thresher.”
Live from Kabul – Election Observation Training

Also, nice report from the NYT, with some troublesome statistics on voter turnout:

Two Claim to Lead Afghan Race for President – NYTimes.com

In the southern provinces like Kandahar, Helmand, Uruzgan and Zabul, turnout was as low as 5 to 10 percent, according to one Western official. That is less than half of what it was in those regions in the nation’s first presidential election five years ago.