There are pro's and con's for both.
I personally prefer punch cards. The main reason is that on some trials, where it isn't mandetory to do all sections in order, you know what you have and haven't done. Also, you know how many you have dropped, it doesn't matter if they get wet, and scores can be worked out whilst the riders are on their final laps (if 2 sets of punch cards are used). Cheating can be done though (if you feel that way inclined) pretty easily, though many clubs use certain shaped clippers for certain section numbers, therefore, this can make cheating obvious.
The boards are good, as it's slightly quicker and the observer doesn't have to move to punch the rider. If they are waterproof it's not a problem, though many aren't. Also, if the observer isn't very observant, he/she can miss your number and sometimes you cannot hear them shout you for it.
I think most clubs go with the boards though, well, they do here in the southwest anyway.