How does a GM use Paizo-style module flip-mats at the table without giving away the entire layout of the level? Take, for instance, Paizo's Emerald Spire Flip-Mat Mega-Pack… wouldn't putting one of these mats down spoil the sense of exploration for the players?
I use sheets of acrylic over top of paper maps and use butcher paper as 'fog of war' - I simply pull the butcher paper out as the PC's move forward. I place anti-slip cupboard liner under the maps so they don't slide too. Works like a charm.
The acrylic sheets are handy when you use dry-erase markers on top, too.
We usually draw dungeons onto a large battle map prior to the session. While it gives away a bit ahead of time, I always found it comparable to have a map of the city (or hiking trail) you visit - it's one thing that you know there is a large round place with a church building around the next corner and a completely other thing to end up on St. Peters Square in real life.
In a RPG session, the interesting thing is the description of what you find and that's usually not appearing on a map.
Other than that I've seen the use of a liberal amount of Post-Its (or plain paper) that gets moved/removed according to the players movement but I find this more of a hassle then it's worth.
In my DM kit I have several 8" x 10" pieces of black felt (purchased at the local hobby store) that I use to cover the parts of the map. I can then reveal the map as players open doors.
We used paper to cover the parts of the dungeon that haven't been explored yet, then pulled them off as we entered the room. I recommend cardstock rather then paper, as I've found paper shifts too easily.