1. Added experimental support for the journal_mode PRAGMA and persistent journal.
2. Journal mode PERSIST is the default behavior in exclusive locking mode.
3. Fix a performance regression on LEFT JOIN (see ticket #3015) that was mistakenly introduced in version 3.5.8.
4. Performance enhancement: Reengineer the internal routines used to interpret and render variable-length integers.
5. Fix a buffer-overrun problem in sqlite3_mprintf() which occurs when a string without a zero-terminator is passed to "%.*s".
6. Always convert IEEE floating point NaN values into NULL during processing. (Ticket #3060)
7. Make sure that when a connection blocks on a RESERVED lock that it is able to continue after the lock is released. (Ticket #3093)
8. The "configure" scripts should now automatically configure Unix systems for large file support. Improved error messages for when large files are encountered and large file support is disabled.
9. Avoid cache pages leaks following disk-full or I/O errors
10. And, many more minor bug fixes and performance enhancements....

A complete list of SQLite releases in a single page and a chronology are both also available. A detailed history of every check-in is available at SQLite version control site.