Next you'll need to install all your favourite plugins. At this stage only activate the plugins that add any value during development. For example, there is no point in activating caching plugins whilst you are building a site as that will only cause problems.
I have listed my preferred plugins below. There are tried and tested, and they work.
The idea behind doing a Seed Site is to save yourself as much work as possible later. So for this reason, even for the plugins that you will leave inactive, you should still temporarily activate them and complete as much of the plugin set up as is possible. Once you have added the plugin's license key (if it has one) and configured the settings (as far as possible), then deactivate the plugin.
Also take this opportunity to update all plugins if updates are available.
If your installation contains any plugins installed by WordPress, then delete those. I mean delete plugins like Akismet. If your host has pre-installed plugins that they require, you should keep those. For example I host with GridPane and they automatically install Nginx Helper and Redis Object Cache plugins and I of course keep those installed.
You will have your own preferred plugin list. Please take a look at my recommended WordPress plugins in case there are any you're not aware of and might like to use.
You should activate all the plugins and add an license keys or settings that will be applicable to all sites. Then you should deactivate all plugins except those that you require for the build of the Seed Site. So for example in my list of plugins you would only keep the ones I have starred active.