Nearly all applications have a common set of requests regarding how you send them to the university. 1) They ask you to write application-specific information about the contents 朱書 (in red). Almost all (but not all) end this with 在中. With only one exception they either ended with 書類在中 or 書類. For kicks, I always threw on the 在中 . I think there are two purposes for this: (1) it helps the post office know what you are sending. (2) It probably helps the administrative staff at the university know what to do with these packages.
Now onto the more annoying (and expensive) feature common to applications. In Japan, you are not allowed to walk over an application. On the one hand, I get that -- you shouldn't be trying to schmooze up the faculty and waste their time. On the other hand, the Japanese solution I don't quite get. This is that you need to send applications by registered mail (書留). The problem is that this makes applications expensive. The price to mail one approaches 800 yen for me.
In the States, registered mail is relatively cheap -- but it's also something rarely used. Instead, you would probably just mail your documents or fedex them. There is a cheaper solution -- one I had mistakenly been using, but which may hurt my chances for jobs where they care greatly for procedure -- Letterpacks. A Letterpack lets you mail something for a fixed 350 yen or 500 yen fee. But it doesn't qualify as 書留 to the schools -- even though it lets you track your package.
I'm not sure what the obsession is with 書留 for job applications (it's not like I'm sending cash or something), but there are two variants of this: 簡易書留 and 書留 where the latter has more features and I believe additional cost. I will be sending out several applications this week and next and will use 簡易書留 where asked by schools -- otherwise I will use up the remaining letterpacks that I bought!