NOTE: See these articles for more details around particular customizations
Customize the Office 365 theme for your organization - https://support.office.com/en-us/article/Customize-the-Office-365-theme-for-your-organization-8...
Composed looks overview for SharePoint - https://dev.office.com/sharepoint/docs/general-development/themes-overview-for-sharepoint
SharePoint Color Palette tool to create spcolor file - http://www.microsoft.com/en-us/download/details.aspx?id=38182
Keep add-ins and web parts on any page to a minimum, you will notice performance issues around 12 objects or so depending on the complexity of those add-ins.
Keep Images, CSS, JS, etc to a minimum
Minimize data requests, or only make data requests at the time of access
Do not make all your data central and then make multiple requests at the sametime
OOB Navigation Stores (MMS, Search Index, or Site Structure) these are simplest to manage or deploy.
Navigation Store API, while very flexible this requires Public Internet resources (SSL, DNS, etc) and particular dev skills
Apply a custom theme/Change the logo
Apply an OOB theme
Create custom Site Columns and Content Types
Custom lists and libraries
Site Configurations (Regional Settings, languages, etc)
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