On Mon, 31 Oct 2011, Mark Rogers wrote:
What is the best way to manage my Android phone with my Linux (U11.04) desktop?
If you're feeling adventurous, it's possible to install Gentoo (or presumably any distro you like) in a chroot on an Android phone - cf. http://forum.xda-developers.com/showthread.php?s=c0a168ade51ea5d435f446cf3ee5508e&t=789003 - then just interact with it like you would any Linux machine.
In the setup discussed on that forum, the resulting Gentoo system has access to the contacts at </mnt/data/data/com.android.providers.contacts/databases/contacts2.db>, and the SMS messages at </mnt/data/data/com.android.providers.telephony/databases/mmssms.db>. Both are apparently in SQLite format 3.