MBRWizard
Small command line utility that can backup and restore the MBR. Can be run from Floppy, CD or within Windows. Has several other useful options, including changing or setting the Active partition and hide/unhiding partitions. Can now also read and write to the disk signature, allowing you to change or backup and restore it.

HxD
Great free hex editor that runs inside Windows and includes raw disk editing, so you can see and change or manually rewrite your MBR Disk Signature.

PTS-Disk Editor
View and edit your Disk Signature from DOS. Thanks to Starman for hosting the download, and the tutorial. (also on the UBCD)

Ultimate Boot CD - (UBCD).
Dozens of useful apps on one CD. Also has the handy option of adding floppy only apps to the CD so you can still run them even if you don't have a floppy drive in the machine. The XOSL bootmanager and PTS-Disk Editor are already included on the disk. Can also be run from a bootable USB memory stick.

EasyBCD
Little app that gives a graphical interface to the Microsoft tools for editing and configuring the built-in Windows bootmanager. Can add Linux, Mac OS X and BSD to the bootmenu. Designed to make it easier to alter the MS bootmanager, but can produce non-native configurations.

VistaBootPro
Another GUI app for editing the Windows bootmanager, similar to EasyBCD.

Partition Table Editor - ptedit.exe and ptedit32.exe
Small app supplied with Partition Magic that lets you view and edit partition tables and boot sector parameters. The DOS version is ptedit.exe, where as ptedit32.exe runs in Windows NT. Both can be acquired separately from Symantec.
ftp://ftp.symantec.com/public/english_us_canada/tools/pq/utilities/PTEDIT32.zip
ftp://ftp.symantec.com/public/english_us_canada/tools/pq/utilities/ptedit.zip
To get ptedit32 to run in Win9x download the following file and extract PQVXD.vxd and place it in the same directory as ptedit32.exe
ftp://ftp.symantec.com/public/english_us_canada/tools/pq/utilities/vfd_folders.exe
Thanks to Ed for this tip.

Gparted
Outstanding Linux partitioning and cloning tool. Obviously won't install in Windows but can be run from boot disk or USBkey. Can do all your Windows partitioning needs and can work to both the old and new partition alignments. It also comes on the PartedMagic bootdisk, which we highly recommend.

PartitionWizard
Excellent Windows partitioning and cloning tool with a free home edition. Can be run from inside Windows, or from boot CD/DVD or USBkey. Version 7.5 has added support for the new partition alinments. Has a couple of minor quirks but don't let that stop you. It always wants to create logical partitions by default and so you have to be careful to select primary. It does not show or mention extended partitions but just makes or extends them in the background as required, but not always as you would want. Has the habit of resizing the extended to include just the existing logicals, thereby leaving any free space at the end of the drive as unpartitioned.