I'm upgrading from Splunk version 3.0 to Splunk 4.1.6. Is it recommended that I uninstall 3.0 before installing 4.1?
You should not uninstall 3.0 unless you specifically want to start completely fresh and lose your customizations, configuration, or other data. Please do note that upgrading from 3.0 to 4.1 can't be done in a single step. In particular, you must run the upgrade to 4.0 first.
http://www.splunk.com/base/Documentation/4.0.10/Installation/Whattoexpectwhenupgradingto4.0
There are very specific steps to upgrading to 4.1 from 3.0. Specifically, I believe there is a pre-migration necessary for going to the latest 3.x release before you can migrate to 4.1.
You should not need to uninstall 3.0 although you should make efforts to back up all data.