This one isn't so much an application, as a suggestion/feature request for the built-in SMS application (perhaps as an alternative, but maybe in addition to what I said above about the phone having a built-in Jabber server):
1) Fully integrate Google Talk and Android's SMS/MMS features. You can use a Google Talk session to send SMS/MMS messages out using your phone number as the source (authenticated some how to keep people from impersonating you), and incoming SMS/MMS messages could be mirrored to your Google Talk session.
2) Have a setting for whether or not you want to automatically save your SMS/MMS messages to your Gmail account's "Chats" folder, along with your other Google Talk chats (as two separate settings, so you can just do your regular chats, just do your SMS/MMS messages, do both, or do neither).
3) Allow your Gmail web session to be used for sending SMS/MMS messages directly, just like you can for Chats.
So, if you're on your laptop/desktop, you'd have the ability to continue your SMS/MMS conversations without interruption, and you'd be able to manage their archiving just like you do for Google Talk.
Bonus if they finally enable Google's Jabber service to do gatewaying to AIM, Yahoo, MSN, IRC, and other Jabber services. Then you could have all of your IM's archived in your Chats folder.