The Predesktop Area is part of the HPA (Hidden Protected Area). The HPA is a special area on your harddisk, usually hidden to partitioning tools. It includes all the software and data needed to recover the preloaded state of the ThinkPad. The HPA also includes some diagnostic tools and a (MS Windows only) backup tool.
The PreDesktop area was introduced with the R/T/X 40 series of ThinkPads and is present on the preinstalled harddisks of all ThinkPads shipped by IBM since then.
General information about the HPA
The HPA seems to be using Phoenix FirstWare. FirstWare is (in short) an implementation of two technologies: BEER and PARTIES. (Yes, those names are correct!) BEER (Boot Engineering Extension Record) is described in this document. There is an introduction to PARTIES (Protected Area Run Time Interface Extension Services) on the IBM site.
Basically, what seems to be going on is that the Phoenix BIOS hides the last few gigabytes of the harddisk (that is the HPA) to the OS. Note that this is just a setting in the BIOS and can be disabled. The HPA can be accessed by pressing the Access IBM Button at boot time. The BIOS will then parse the BEER and the "Directory of Services" (situated in the last sector of 512 bytes of the harddisk) to see what part of the HPA should be launched. In (most?) ThinkPads the BEER and the Directory of Services tell the BIOS to launch the Access IBM Predesktop Area. The system will then actually be booting into a (minimal) DOS which is able to launch a graphical shell (called Phoenix FirstSight). IBM has simply rebranded this graphical shell to the Access IBM Predesktop Area. From this graphical shell one can launch several tools (BIOS Setup Utility, diagnostic tools, recovery tools).
How to remove it
There's a BIOS setting in my T42p. After disabling the Predesktop Area, it's possible to remove the partition with standard tools. i.e. fdisk, mkfs, ...