My group (D&D 3.0) has used an old hex mat for years. We never really liked it, but it was what we had, so we used it. The main thing we didn't like was trying to draw rooms on it in any way to scale. We were always asking questions like "can I stand here? It's only a half/third/quarter of a hex." And that was when we tried to draw square/rectangular rooms!
Then we switched to a more traditional square board that I made out of a large sheet of transparant plastic. We've only played on it a couple times, but the DMs seem to like it (easy to draw rooms, etc...). Our only unexpected problem was movement. Specifically, diagonal movement. For those who don't know about this problem, it has to do with the squares being larger across the diagonal then they are on the edge. If a character moves 6 squares forward, they've traveled 6 inches (or 30' scale). If they move 6 squares diagonally, they've moved ~8.5 inches, or 42.5 feet. This makes moving diagonally tactically superior to moving straight unless it's somehow taken into account. I've read different solutions to this problem on the boards. The easiest is to count a diagonal move as 1.5 squares, so if you can normally move 6 squares forward, you can move only 4 squares diagonally. This works pretty well, but what if you move one square diagonally and "the rest" of your moves forward? You end up trying to move forward 4.5 squares! The only really fair way to handle the problem (which is a handful) is to measure your movement with a ruler. If you movement is 30', you can move 6" in any direction. This also breaks down, though, if your character is moving in anything but a perfectly straight line. If they have to move around other characters, avoid threatened spaces, etc, measuring doesn't help much at all.
Hexes don't really have this problem because there are no diagonal lines. Other than the diagonal problem, we have enjoyed squares for their tactical precision. I'm going to recommend the diagonal move = 1.5 squares to my group tonight.
