2000 was not a normal election.  People say 9-11 changed everything, but 2000 may have been just as traumatic.  No American could remember anything like it in their lifetime.  It simply did not happen in America.  It simply could not happen.  The USSC chose the President.  It is my opinion that there is funny business in every election, probably in ever country.  But what happened in 2000 was a bit of an anomaly.  Not because it was unfair, but because of how it was resolved, which has left everyone with the feeling that American democracy is a joke.  But there are elections in this country every year, throughout countless municipalities, counties, states, etc.  And it appears, given the way people are going to the polls like never before, the American people have rethought their opinion that our elections are a joke.  NB:  If Obama loses, it's going to be ugly.  It will def. be another nail in our coffin.  But it is important to remember 2000 in Florida, while it changed the course of world history, was one election, one state, a few counties.

Now, not counting all the votes.

You could be referring to 2 different things.

1.  The way the media does not wait until all the votes are counted before calling a winner, based on statistical probability.

or

2.  The way voting machines discard ballots they consider "invalid."  Some systems are set up so that an "invalid" ballot is caught when the voters scans it, and some people cast their ballot not knowing that their ballot will be considered "invalid."  What constitutes "invalid" varies by machine, and is offensively arbitrary.  But it remains a very small percentage of ballots that are considered "invalid", from what I have seen as a poll watcher.

However, every valid ballot is counted.  Election judges are locked in the polling place when the doors close, and must stay until the votes are counted.  They usually compare the computerized tally to a hand counted sample to make sure there was no hacking or computer errors.  Then the tape listing all the votes and the official tally (looks like a cash register receipt tape roll) is given, by hand to the ... uh, election commission, board of elections, I don't know, whoever runs the elections, and a duplicate is posted publicly.  Or, that's how it works here.  So you don't hear about it, but all the votes are actually counted, in my experience.  Above, I noted that there is no standard way of doing these things, so it could be different elsewhere.  But all votes considered valid are counted at each polling site in my experience.  

"Pretending that you already know the answer when you don't is not actually very helpful." ~Migeru.