I've not changed/added any plugins since the WP 2.9 upgrade.
Here is what I've got installed: Akismet
Akismet checks your comments against the Akismet web service to see if they look like spam or not. You need a WordPress.com API key to use it. You can review the spam it catches under "Comments." To show off your Akismet stats just put <?php akismet_counter(); ?> in your template. See also: WP Stats plugin.
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Version 2.2.7 | By Matt Mullenweg | Visit plugin site
FD Feedburner Plugin
Redirects all feeds to a Feedburner feed
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Version 1.41 | By John Watson | Visit plugin site
Google Analyticator
Adds the necessary JavaScript code to enable Google's Analytics. After enabling this plugin visit the settings page and enter your Google Analytics' UID and enable logging.
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Version 6.0.2 | By Ronald Heft | Visit plugin site | FAQ | Support | Donate
Google Custom Search Plugin
Integrate Google Custom Search into WordPress
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Version 1.2 | By Aleem Bawany | Visit plugin site
RefTagger
Transform Bible references into links to the full text of the verse.
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Version 1.6 | By Logos Bible Software | Visit plugin site
ShareThis
Let your visitors share a post/page with others. Supports e-mail and posting to social bookmarking sites. Configuration options are here. Questions on configuration, etc.? Make sure to read the README.
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Version 3.2 | By ShareThis | Visit plugin site
SI CAPTCHA Anti-Spam
Adds CAPTCHA anti-spam methods to WordPress on the comment form, registration form, login, or all. This prevents spam from automated bots. Also is WPMU and BuddyPress compatible. Settings | Donate
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Version 2.2.6 | By Mike Challis | Visit plugin site
Smart Youtube
Insert YouTube videos in posts, comments and RSS feeds with ease and full customization.
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Version 3.3 | By Vladimir Prelovac | Visit plugin site
Subscribe Remind
Give your readers a little reminder to subscribe to your blog's feed at the end of each post.
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Version 1.2 | By Trevor Fitzgerald | Visit plugin site
Subscribe To Comments
Allows readers to receive notifications of new comments that are posted to an entry. Based on version 1 from Scriptygoddess
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Version 2.1.2 | By Mark Jaquith | Visit plugin site
Tweet This
Adds a "Tweet This Post" link to every post and page. Shortens URLs. Can automatically tweet new and scheduled blog posts. Highly customizable.
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Version 1.6.1 | By Richard X. Thripp | Visit plugin site
Twitter for WordPress
Displays your public Twitter messages for all to read. Based on Pownce for WordPress by Cavemonkey50.
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Version 1.9.7 | By Ricardo González | Visit plugin site
Woopra
This plugin adds Woopra's real-time analytics to any WordPress installation. Simply sign up at Woopra.com, then activate the plugin!
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Version 1.4.3.1 | By Elie El Khoury, Shane Froebel | Visit plugin site
WordPress Database Backup
On-demand backup of your WordPress database. Navigate to Tools → Backup to get started.
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Version 2.2.2 | By Austin Matzko | Visit plugin site
WP Greet Box
Show a different message to your visitor depending on which site they are coming from. For example, you can ask Digg visitors to Digg your post, Google visitors to subscribe to your RSS feed, and more! Best of all, this plugin is compatible with various WordPress cache plugins.
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Version 5.5.5 | By Thaya Kareeson | Visit plugin site
WP Super Cache
Very fast caching plugin for WordPress.
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Version 0.9.8 | By Donncha O Caoimh | Visit plugin site
Youtuber
Easily add YouTube videos to posts using valid xhtml markup.
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Version 1.4 | By Roy Tanck | Visit plugin site