Is there a way to edit the registry from a command prompt (DOS)?

Unfortunately, because the registry is a part of Windows, it is not possible to edit the registry without running Regedit through Windows. If you are not able to get into Windows, you may wish to attempt to run regedit.exe from Safe mode.

How can I clean out old data from the Registry?

Although it's possible to manually go through the Registry and delete unwanted entries, Microsoft provides a tool to automate the process, the program is called RegClean. RegClean analyzes Windows Registry keys stored in a common location in the Windows Registry. It finds keys that contain erroneous values, it removes them from the Windows Registry after having recording those entries in the Undo.Reg file.

Description of the Windows Registry

The Microsoft Computer Dictionary, Fifth Edition, defines the registry as:
A central hierarchical database used in Microsoft Windows 9x, Windows CE, Windows NT, and Windows 2000 used to store information necessary to configure the system for one or more users, applications and hardware devices.

The Registry contains information that Windows continually references during operation, such as profiles for each user, the applications installed on the computer and the types of documents that each can create, property sheet settings for folders and application icons, what hardware exists on the system, and the ports that are being used.

The Registry replaces most of the text-based .ini files used in Windows 3.x and MS-DOS configuration files, such as the Autoexec.bat and Config.sys. Although the Registry is common to several Windows operating systems, there are some differences among them.
Registry data is stored in binary files.

Description of Linux Registry

The Linux Registry is a toolkit that provides a programmatic registry for Linux applications. The term "registry" is taken from Windows, but the idea dates back to at least NeXTSTEP, which had a similar concept. The idea is that persistent properties are managed by a simple library and are available to applications for setting configuration data in a consistent manner. Read the main Linux Registry page for more in-depth reasons as to why this is a good thing.

This project, in particular, provides a Ruby binding for the Linux Registry, providing an easy API for accessing registry variables.