When using a service such as Dropbox or Mozy, this can dramatically slow down backups -- a single change to your iWork document means the entire single file must be updated again. Using the old format, the backup updater can read each piece of the file as a separate entity, so if only part of the file is modified, it can back up only those parts that need to be changed, making it much more efficient. This is especially noticeable with large Keynote documents, which can be hundreds of megabytes.
To get the old formats back, simply go into Preferences in each iWork application, and under the General tab, check the box that says Save new documents as packages.
Note that when saving as packages, there is no longer an easy way to recover individual versions of the file using Dropbox. That's because the file is treated as a folder with individual files inside; you could theoretically revert each individual file manually, but it would not be as easy (Time Machine's versioning is not affected). Also, I do not know of a way to convert existing iWork '09 documents to the package format.
[robg adds: There's more discussion on the new iWork file format in this hint and associated comments. You can't convert one document to the old format using Save As; I tested it with Pages, and even after changing the prefs, it still saved as a single file.]

