God, you people have it all wrong.
First off plan for a long day at Kinkos.
Second is copy each page of your manuscript, then laminating each page (both sides). This way when the agent spits coffee over your beautiful prose, the agent will be able to wipe the page off, hopefully leaving your prose in pristine shape. Never mind that this is expensive and takes time -- your writing is worth it. The fact that the agent can't make notes on the paper is not your concern.
Third is take each chapter and bind it carefully in rubber bands. You need ten rubber bands length wise and five rubber bands width wise. Remember, rubber bands break, and you want to err on the side of caution. Never mind that the agent will get irked at all the rubber bands, protecting your valuable manuscript is important. After you have all the rubber bands on, carefully wrap each chapter in plastic wrap. At least five layers so if there is any rain it won't get through to your perfect book. Remember that making sure your document is perfect is important. And the agent is going to be impressed by all the care you've exerted.
Fourth, take all of your chapters and strap them together with the strapping used for boxes of paper. Again, a ten by five system works well here. You don't want a strap breaking and causing problems. Remember, protection of the world's next best seller is paramount here. Take the entire manuscript and wrap carefully in bubble wrap. Multiple layers so that if the shipping container is punctured, none of your brilliant words will be compromised.
Now we can move onto the shipping container. Some people feel that there is a choice involved here. Some people feel that a one-inch oak chest is enough, screwed closed. Others feel that a quarter-inch steel case, welded shut, is the best choice. Both are in fact wrong. You start off with the oak chest and insert it into the steel case, making sure that the entire package is air and water tight.
Shipping agent can be a difficult choice. Some people believe that the post office works, while others swear by FedEx. Personally I know people who have sworn at both, as their manuscript gets lost or damaged in the process, causing an agent to reject it. Personally I believe that driving it to the agent is the only route, especially if you have to go overseas. Remember that you have to keep visual sight of your precious writing no matter what. Sleep is dangerous, as someone might steal the next Pulitzer prize winner, to publish it under their name.
Following these steps will guarantee the agent will be amazed at the care with which you've delivered your priceless manuscript. The agent will be able to make a decision sight unseen, as no one but a special writer would go to this extent to protect their manuscript.
Best of luck,
Jim Clark-Dawe