In the latest releases Parcellite claims to support Unity. Debian packages without an application indicator are available from the project's home page. There we also have an announcement for a ppa that is supposed to contain the application indiciator once it is populated.

Alterantively you may install its fork ClipIt instead.

In case you do for any reason need to further run Parcellite you may whitelist its panel icon by running dconf-editor (from dconf-tools ) Desktop -> Unity -> panel or from the command line

gsettings set com.canonical.Unity.Panel systray-whitelist "['parcellite']"