The worst situations with airline checkin counters happens when there is a problem with cancelled or delayed flights and lotx of pax need to have their reservations changed.
There was a thread recently on the reasons why paper tickets are better than e-tickets. One of the upsides to e-tickets is that many airlines have installed kiosks for check-in that usually reduces the wait time, even with luggage.
Airlines really don't have an excuse for understaffing airport counters in airports where they have a large presence with many planes coming through during the day. The NW lines at MSP, for example, are either very long or very short -- rarely in between. It would be interesting to build a simulation model of an airport checkin area with all of the various things that happen that affect the amount of time (service time) for each customer, and an arrival rate that has the unusual pattern of heavy arrivals for the hour before a flight, then little until an hour before the next flight.