1. Don't go in summer. Besides that summer's one of the most expensive times to travel in Japan, the weather is miserable, especially in Tokyo. Also, you wouldn't want to be there if the air conditioning breaks, like it did in the summer of 1998. People were passing out from the heat and CO2 poisoning! I'd most recommend winter Comiket, if you have an option. As one friend pointed out from experience—it's much less likely to rain in December, as opposed to August.
2. Buy your guide book ahead of time. This is all you need to get in, but it's much more convenient to not have to buy one there. Plus, if you have it in advance, you can better plan where you’re going. There are plenty of places which sell them, including most branches of Manga No Mori, Shosen, Animate, Too, Yurindo, Sanseido Book Center Manga Ou, and Hourindo, though I have no idea how many of these are still open. Also, one friend has reported to me that he could not buy a guide book at Comiket because they were sold out. Another reason to get yours early!
3. Wear comfortable shoes. This is generally true of traveling anywhere in Japan, but it's especially true of big dōjinshi events. I also recommend dressing nicely but fairly comfortably; people tend to dress nicely for these events even though the floor is often the only option for sitting.
5. If you take a train, be sure to buy your return tickets from Comiket when you arrive so you don't have to wait on the way back. The lines will be atrocious all day, so be ready for this. Crowding may force you to wait for the next train or bus, both going and coming.
6. Bring something that makes carrying lots of heavy books easy. It's quite common to see people with luggage carriers, loaded with boxes of dōjinshi. Actually, a luggage carrier can be quite convenient, if you're shopping with a group. Though you will see shipping stations here and there around the event, they are only for domestic shipping, not international.
7. Bring cash. This is generally a good thing to do anywhere in Japan, but in my day none of the vendors would take anything but cash. Try to have primarily 1000Y bills for convenience.
8. Bring lunch. There's hardly anything available to eat and, like most convention centers, the food is mediocre and expensive. There was a Sun 'K' Us (a convenience store) between Big Site and the station along the bridge/elevated walk. However, you can never be sure about availability when you're dealing with crowds of over 100,000 people.
9. Make a plan ahead of time. Know which places you want to go to first and learn their locations on the map. If you're going with other people, choose a meeting place and times, in case you lose each other in the crowd. If you plan to eat lunch there, be sure to do it. The crowd is carrying germs from all over Japan; being underfed that day is not a good idea. Try not to need to use the restroom; lines can be up to 90 minutes long, especially for ladies.
10. Go early. These events start early and end by 2PM. Most places start packing up by 1, so don't think you'll be able to sleep in that morning!
One last thing: Don't take any pictures indoors; it's not allowed. There will be an area outside for photographing people in cosplay. Be polite and ask (onegaishimasu) before you take a picture and thank them (arigatō gozaimashita) afterward.