TweetDeck added an option recently (I'm not really sure when, I for one only noticed this today thanks to NicoLargo) to add a custom Twitter Base URL. Using this option, you'll be able to use Identi.ca in TweetDeck.
Install AdobeAir in Ubuntu
Ubuntu - 32bit:
AdobeAir is available in the Ubuntu Partner repository so Ubuntu users (32bit) can install it from this repository:
1. Press Alt + F2 and enter:
Then on the "Other Software" tab, enable the first repository (the one which says "partner"). Then click "Close and when prompted, click "Reload".
2. Search for Adobe Air in the Ubuntu Software Center or install it using a terminal:
sudo apt-get install adobeair
Ubuntu - 64bit:
1. 64bit Ubuntu users must install ia32-libs:
sudo apt-get install ia32-libs
2. And then download the Adobe Air .deb from Adobe's website and install it with:
sudo dpkg -i --force-architecture adobeair.deb
Once you've installed Adobe Air, simply go to the TweetDeck website and click the Install button.
Use Identi.ca in TweetDeck
And now finally you can set up Identi.ca in TweetDeck. Once you start Tweetdeck, add your Twitter account (or skip this), then go to the TweetDeck settings, then on the Account tab click: Add New Account > Twitter, then click "Advanced options" and enter the following URL:
In the username and password fields, enter your Identi.ca username and password and then save the settings.
Now you can enjoy both Twitter and Identica in TweetDeck.
Many thanks to NicoLargo for the info!