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@Dominik Bartholdi:
Thanks for the hint. That plugin does indeed give me a chance to get around the problem without any fancy JVM keystore work; though one has to be aware that of course it does disable all SSL cert checking, which is a different goal than to make sure you trust your self-signed certificates, which is what would happen if you go for Mark Waite's suggestion (essentially to use JavaSSL.zip, http://demos.erikzaadi.com/jenkins/JavaSSL.zip).
BUT there are still two things to watch out for:
1. You need to use JGit. If you use the platform native git binary, you will fail (tested with git-client 1.9.1 and git 2.2.2). Funny enough, you will fail somewhere in the JVM, i.e. something in Java tries to do SSL certificate validation (obviously bypassing the Skip Certificate Check Plugin) while you have opted to use the native platform git.
2. Even if you use JGit, the above mentioned issue will lead to an error message in the job configuration dialog like this:
<code>
Failed to connect to repository : sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
</code>
But one can safely ignore it an just go on. The job will clone properly when run as long as you make sure you use JGit in Jenkins. On native git, the error message will be the same, but your clone will break somewhere half-way. (Check the workspace of your job after it broke.)