A quick Google found this page about how to upgrade but my question is how do I make sure all configurations remain intact (Samba, Apache, SVN) and also, is it worth it to upgrade? Will 9.10 continue to have bugfixes/security updates and the like released to it via the package managers?
As part of the package upgrade process, if you have modified a configuration file you will be asked if you wish to keep the modified file, or install the new version, and have the opportunity to view the differences.
This wiki page shows the support periods of all the Ubuntu versions - wiki
Standard releases, e.g. 9.10, are supported for 18 months. LTS releases are supported for 3 years on the desktop and 5 years as server. Upgrading to 10.04 has the advantage of this being LTS.
9.10 will continue to have security and regular bugfixes released until April 2011. The server version of 10.04 will have fixes released until April 2015 as it's a Long Term Release (LTS). At the moment your covered but you will have to upgrade from 9.10 after April 2011 if you wish to receive security and regular updates.
I've always chosen to do clean installs when upgrading versions and saved my configuration files separately so I'm unaware if upgrading will overwrite configuration files.