The Afghan elections did not meet the catastrophic failure of total disruption and violence that many officials feared. That hurdle, at least, was cleared, and most people are carefully avoiding entertaining the idea that most of the Taliban (remember they are not always a united front) did not care too much about the elections. That is not to say that there was not violence; there were rockets, there were roadblocks, there were mortars. But they were sporadic and isolated--had the Taliban been bent on preventing the elections from happening, much more noise would have been made.
But that's only one hurdle. Turnout was apparently significantly lower than the last election, especially in the south, probably due largely to Taliban intimidation tactics. This southern area is dominated by Pashtuns, where Karzai seeks much of his support to beat Abdullah. Whether this disparity in turnout will affect the election, and whether it will call legitimacy into question, is unclear.
Other problems include complaints of ballot-stuffing or other issues of corruption. Karzai's power over Afghani bureaucracy is massive, and has led to a great deal of corruption and graft in normal government functions, and is almost certainly going to leak into the election, even if Karzai himself does not intend to cheat.
Beyond that, the Independent Election Commission (IEC) has to deal with inflated versions of normal election problems, like hanging chads.
But the votes are indeed being counted. Both Abdullah and Karzai have claimed victory, but the IEC has said that it's too early to tell. A Voice of America survey of three polling districts in Kabul put Karzai ahead in 2 of them, and Abdullah ahead in one, and neither with a majority. Ghani and Bashardost were in 3rd and 4th--Bashardost was unable to leap past fourth place even in his own district of Kabul.
Karzai will fare better in the south, and Abdullah better in the north. Karzai's primary disadvantage will be the low Pashtun turnout, but he makes up for this by a number of deals cut with warlords and other local leaders in the north. It should be a close race, and I think a runoff is likely.
Unfortunately, a runoff will be a logistical nightmare of the same magnitude as this election. The Taliban will be able to pose a similar threat, the US will probably have to spend another $250 million on it. If Karzai or Abdullah win outright, there will at least be a sigh of relief that the mess is over for a few years. That said, an outright Kazrai win would likely lead to a number of calls of corruption, irregularity, etc, and hinder reconciliatory efforts across the country.
Should a runoff occur, the two big bargainers will be Bashardost and Ghani, whose support should be able to deliver key slices of vote. I predict that they'd be more likely to support Abdullah, who shares their anti-corruption message, but Karzai is a great negotiator with a lot of power, and could sway them to his side. Should Karzai lose, his supporting warlords will have also lost, and will have little in the way of loyalty to the new government. Whether Karzai can or will convince them to get in line will be worth keeping an eye on.
More updates as we get them.
(P.S.: Congratulations and thanks in particular to the US and UK troops that have, for the past two months, helped prepare southern Afghanistan for an at least semi-functional voting experience. The impact on the local population is likely to be critical.)