Moneydance 2012 uses a new checkpoint system for backups. For more info on where your Moneydance 2012 data file is stored go here.
Moneydance 2011 and earlier can be set up to save backup files, and automatically saves the last 5 backup files in the same location as your data file. These files are regular Moneydance files with either the date or a tilde (~) appended to the '.md' file extension to keep you from confusing them with your regular files. To open such a backup file, simply rename it so it ends with .md and you'll be able to open the file and access your transaction history as it existed in Moneydance at the time of the backup.