Generally speaking, you are only linking to other resources on the web, and generally that's not illegal. But that could be different depending on the country that hosts the site and the country of the user's access.
This site seems to have no problem: http://thehiddenwiki.org/hidden-wiki/ Read their TOS, too: http://thehiddenwiki.org/2013/06/26/terms-of-service-and-privacy-policy/
That site is hosted in Romania (the domain is privately registered in Malaysia), but Germany and Romania are both EU.
Now, what users may use those links for may be illegal. And that's still in legal flux in some jurisdictions, i.e. the hosting of a site of BitTorrent links that allow downloading of copyrighted material while the link itself does not contain the material themselves. See https://en.wikipedia.org/wiki/Legal_issues_with_BitTorrent
Besides, a list of .onion links on the regular web is useless unless you know how to use the links; you're linking to resources on the "dark" that are not even directly accessible from those links on the "bright" web.
Someone who wants to go to an .onion link needs to install Tor https://www.torproject.org/ to enable the DNS changes to access the .onion TLD (Top Level Domain). .onion is not even in the Internet's Root Domain; it's a special case TLD. https://en.wikipedia.org/wiki/.onion
Installing and using TOR is one more step that someone has to take to make use of a link in the "bright" web to reach a link in the "dark" web. So your links are "isolated" in one more sense from usefullness, and that could be a legal defense, if it even comes down to it.
Like anything, do your own research and draft a good TOS for your site.
And, at the same time, using TOR is not illegal itself (but could be in some countries), but can result in illegal activity: https://en.wikipedia.org/wiki/Silk_Road_(marketplace) Read TOR's own legal FAQ: https://www.torproject.org/eff/tor-legal-faq.html.en
