Both Mendeley and Zotero have a few lacking features for me (lack of decent iPad apps for both, lack of a metadata lookup function for Zotero), so wondering if there are better alternatives that HN users could recommend. For a non-free option, ReadCube Papers is a possibility, but I've yet to try it.
JaBref. I don't know whether it works on iPad, but it does the job for me, has many custom export filters and it's dead easy to write your own export (I do it for yearly reporting in arcane format).
Icing on the cake: the storage format is just a *.bib file that can be shared, versioned using git, ...