I need to access custom segments in Google Analytics via reporting the API. There is no trouble with it, except that custom segments are not shareable across multiple profiles/users set in Google Analytics, so a segment has to be created for each profile.
And in the case of using a Service Account generated through Google API's Console, segments have to be created for that account – how do I log in to Google Analytics with a Service account having Client ID, email address and public key fingerprint to be able to set segments for it?
It is not currently possible to create segments with the Google Analytics Management API.
Edit:
As of July 9, 2013 Google Analytics added access to custom dimension and metrics. Now it is possible to query custom dimensions without the need to create additional segments, so the roots of my problem have disappeared.
It currently is not possible to create segments for a service account. As you suggested you'd need to be able to login to the GA account to create it, which is not possible with a service account. The only option right now is to use dynamic segments when querying the Core Reporting API.