If you use the Thesis theme framework, then you should have noticed no negative side effects after upgrading to WordPress 2.9 (or 2.9.1).
The only issue that I have found is that WordPress now has basic canonical URL handling. Why is that an issue?
Thesis has had more complete canonical address handling for quite some time now, pretty much since canonical addresses were just starting to be hip & cool.
And while Thesis has an option on its options page to disable its canonicalization, we shouldn’t sacrifice the more robust option. Instead, add this piece of code to your custom/custom_functions.php file, which will disable WordPress’ canonical URLs.
# Remove WordPress' canonical links in preference of Thesis'.
remove_action('wp_head', 'rel_canonical');