Sysinternals RegistryUsage is a tiny command line tool which can tell you more about which of your Registry keys are consuming the most space.
Pass the program a specific path, for instance (like "ru HKEY_LOCAL_MACHINE\SOFTWARE\Windows", although short paths - "HKLM" - are also supported), and it'll scan the Registry for a few moments, before reporting on the number of values and keys within that path, and their total size (in bytes).
Other switches allow you to define the level of subkey information you need, whether you want to see the size of each subkey, and so on.
If ru is producing way more information than you can examine in a command line window, there's also an option to format its output as CSV, with optional tab delimiters.
And as usual, just launching ru with no switches will display helpful information on the various options you have.