I know of only one way that this can happen in windows, and has nothing to do with Steam other than their not-so-great decision to install all content into Program Files.
If you are on Windows 7 or Windows Vista, and you have UAC set to ON, then change it later to OFF, this can happen.
UAC does thing evil thing where if a program tries to write to a "protected" area like Program Files, EVEN IF YOU ARE ADMINISTRATOR, when you get a UAC prompt and give permission, it actually writes any files that would normally go into that directory into a "virtualized" directory somewhere else.
If you turn off UAC, that will no longer happen, and as an awesome bonus, it will no longer know about the files that it virtualized.
So in your case, if you had UAC on, installed a ton of games, then later got sick of UAC and turned it off, this would happen as you described.
See the second paragraph in "Features" in the article on User Account Control.
If you have done this and turn on UAC again, your content will come back, but be a TOTAL mess because if you've downloaded more stuff with UAC off, then that will be invisible when you turn UAC on, and vice versa.
this drove me a little crazy once before I realized what was happening.
i'm curious to know if this is your issue.
I know this is an old question, but for future generations:
Copy Steam_directory/userdata/your_long_number/7/remote/sharedconfig.vdf between computers or back it up.
Steam_directory is~/.local/share/Steam/ on linux, ~/Library/Application Support/Steam on mac, and wherever you chose to install Steam on windows (usually C:\Program Files\Steam or C:\Program Files (x86)\Steam).
Best Answer
If there is a conflict with the save files, Steam will ask you whether you want to keep the cloud saves or local saves. This will occur with every computer that has greatly different save files.