I have voted in a lot of different states, but the way we do it here in my current district seems to work well. I got my ID checked against the voting record -- the lady may an explicit check to make sure the addresses matched. Then I got a paper ballot and a black magic marker. Next to each name is an arrow pointing to the name with a gap in it. One fills in and completes the arrow pointing to the candidate one is voting for. Then, when done, the voter takes the ballot to a machine that looks like a big shredder. She/he feeds the ballot into the slot, and the ballot is automatically read and counted right there. There is a LED readout on the front with a total ballot count that increments by one if the ballot is read correctly, providing a psychologically satisfying feeling that one's vote has been counted. At the end of the day no further counting is required, and I presume they pull the vote counts out electronically or with some kind of summary report. The ballots stay in a locked vault in the scanner and provide a paper trail if the count has to be checked later.
By the way, no line at all. Glad I didn't wait 2+ hours last weekend to vote early in order to avoid the lines. One has to wonder at the decision-making ability of folks who waited hours to vote early to avoid lines that couldn't possibly be any longer on election day. Good to see such folks out voting ;=)