Best file manager: GoodReader
Many people really wish the iPad had a shared file system like a PC or Mac, but it doesn't. GoodReader can give you much of the file manager you want. It provides a central file repository for files you transfer via Wi-Fi, various storage services, iTunes, and the Open In facility used by many iOS apps (such as Mail). GoodReader -- as its name implies -- also lets you read many file formats, including several not supported by iOS's naive QuickLook facility. Plus, it unzips file archives, so you don't need a separate utility for the task.
Compatibility: iPad (iPhone version: $4.99)