We have started a significant effort to move our theming which has been 100% custom made in the past in a more standardized way. We are building a Linchpin Theme Plugin that will help our customers and partners to make all changes to the Linchpin Intranet interface on their own while staying update-compatible and in a low-maintenance mode.
We are gradually rolling out an alpha test of this plugin at this moment to partners and internally. If you are interested in finding out, what theming in Linchpin will look tomorrow, we're more than happy to provide you with a copy and a short intro on how to use it. Just contact us.
The plugin is planned to be very low cost or even free on the Atlassian marketplace in the future.
You may also want to read our answer to this question as it is related.