Should be safe to run on your home dir or root “/” folder, but running on your home directory should do wonders for you in terms of disk space and speedup of various applications. The name patterns of which files are sqlite databases is a constant on-going tweek so can’t say for sure this catches all of them. You’ll see a few “not a database or encrypted” errors coming from sqlite which so far seem be safe to ignore from what I can tell.

#!/bin/sh
find . -type f \( -name \*.db -o -name \*.sqlite -o -name \*.sqlite3 -o -name \*.syncdb \
-o -name \*.changedb -o -name \*.synciddb -o -name \*AvailableFeeds\* -o -name \*DefaultCounts\* -o -name \*Envelope\* \) -exec sqlite3 {} VACUUM \;