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I am planning to upgrade my OS to the latest version of Ubuntu. I would like to retain some of my configuration files and startup scripts. Can someone please tell me what is the best way to do this? I mean what directories to make a backup of so that there are minimum clashes?

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Use the update manager. Upgrade to 9.10, then to 10.4 (direct upgrades are not supported). This will retain all the configuration changes you've made, unless the program has changed in some incompatible way.

The important files to back up before an upgrade are in /etc. You may also want to back up your user settings (files and directories beginning with a . in your home directory), as the new version of the GUI sometimes screws up your old settings; but you back up your home directory regularly anyway, right?

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Just as a note - before doing this do a quick search on google for Ubuntu upgrade your version numbers to and from and your computers name particularly if it is a laptop so you can know what problems to expect. – srboisvert Aug 19 '10 at 16:02
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When I upgraded from 9.04 to 10.04, I used the built-in upgrade feature. It kept all of my server settings - samba config, static IP, fstab, inittab, apache, mysql, probably more.

If you are really worried, you can tar up a few dir's in case they are overwritten. However, I'd be careful to not overwrite a newer version of a system or config file. Startup scripts are generally located at /etc/init.d.

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