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Overall OneNote tends to be a very reliable product but on occasion you may run into an issue or two. Here are a few tips for getting that resolved.
One quick troubleshooting step you can take with OneNote is to start it with the /safeboot switch. Start | Run | Onenote /safeboot. OneNote will start and present you with a couple of troubleshooting options. One of these options is to clear the OneNote cache (see below) and the other is to clear the customized user settings, which basically resets OneNote back to the default.
OneNote uses a local cache file to improve performance, reliability and sharing. All work in OneNote is actually done to the local cache file rather than the actual data file and then those changes are quietly sync'd to the data file in the background.
Sometimes the cache in OneNote 2007 can get corrupted and the best way to troubleshoot it is to delete it. Assuming all of the changes you have made have already been committed to the data file deleting the cache will not lose any data - but if you're at the point where you're deleting the cache file you're probably fairly desperate anyhow so a little bit of data loss may be an acceptable price to pay to get the application back on its feet.
The cache file is typically found in the: C:\Users\[username]\AppData\Local\Microsoft\OneNote\12.0 folder if you're running Vista or the C:\Documents and Settings\[username]\application data\local\Microsoft\OneNote\12.0 folder for Windows XP. With OneNote closed, using Windows Explorer go to that folder, find the OneNoteOfflineCache.onecache file and either rename it, move it or delete it. I usually recommend renaming it so that if this fix doesn't work and you decide you want to you can always rename it back.
When you start OneNote it will automatically recreate the file; hopefully without whatever corruption caused the problem.
If neither of those steps help then you might need to repair OneNote's installation. In OneNote 2003 you could click Help | Detect and Repair to do a repair install (or if OneNote wouldn't start you could initiate that process from any other Office 2003 application like Word). With OneNote 2007 and 2010 you need to go to Control Panel and to the Add/Remove Programs (or Programs & Features if you're using Vista or Windows 7) find Microsoft Office (or OneNote if you installed it by itself) and run the installer. It will offer you options including Uninstall or Repair. Choose Repair and let it run through that process.
Witth OneNote 2007 and 2010 you shouldn't need your installation media. With OneNote 2003 you probably will need it.