An easy one that I have done for clients is simply different colored cards. If you only have two meal options, it's very simple. Say your colors are brown, apple green and cream. You can do cream for the main dish and apple green for the vegetarians, and write the names with a deep chocolate brown ink. If you have more than 2 options, you can always incorporate another color as well.
Another simple way is to punch a tiny hole at the top right or left of the card, and tie a colored ribbon. So taking the same color scheme above, you would then have all cream cards, and leave the dish with the highest number plain (for this we'll say it's fish), tie an apple green for vegetarians and a chocolate brown for the beef option. For both of these options, make sure that the colors are far enough apart so that the catering staff can easily tell the difference.
We have also used really cool stamps from places like Paper Source, tied a simple card from the back of each chair (this is best when done with the different colored cards) or put an adornment of some type on the different cards (this can be pressed flowers, rhinestones or other small objects that can be glued on).
Whatever you do, just make sure you communicate this with your caterer so they are aware of the codes, and your wedding meal will be served smoothly.