You can rebuild the embedded SQLite database for a server by clicking the arrow icon on the left panel next to the server name and selecting the Rebuild Database option. Using this option periodically may result in better performance - including shorter startup time when OS is rebooted. Basically using this option defragments the database including indexes. It is not possible to provide an absolute advice on how this option should be used. But the larger the databases and the shorter the sample interval the faster there is a chance of fragmentation occurring after a huge amount of INSERTs and DELETEs to the database (Only with databases files of around 1 GB and larger we have seen the need for this. A general advice could be to execute monthly with large database files).
Also note, if the error "Database or Disk is full" (on Windows) prompts when VACUUM is executing, it refers to the file system hosting the temporary files location. Try setting the TEMP environment variable to a location with more free space, restart your system and it works.
Location in Windows 2008: