Piwik allows to upload your custom logo, which will be displayed everywhere the normal Piwik logo displays:
1) top of the screen in the Analytics reports,
2) Login screen,
3) Emails & PDF Reports.

To upload a Custom Logo in Piwik, login as the Super User, click on Settings > General Settings > Branding, and click on “Use a custom logo”.

If you are interested to customise Piwik further, see this FAQ: Piwik White Label offer.