Hi Thomas,
We haven't found an open thesaurus for engineering that works yet - Inspec has one, but it's subscription. The PLoS thesaurus is open and covers engineering, but it's not very deep because they don't publish a great deal in that area.
We want results for every paper because concept tagging provides inputs to processes that we perform on all papers (finding editors, finding reviewers, related papers, search, etc.) We don't want these processes to work better for some papers than for others.
We do use MeSH everywhere we can. When we can't, one solution is just to build a new scheme and publish it, as PLoS has done, integrating MeSH concepts into a larger vocabulary. This isn't so much a problem for us, it's just inefficient: all publishers are working on this problem now and building parallel but not exactly equivalent vocabularies.
This is less elegant than if we used the same open vocabulary for all of science (way easier said than done). I'm not a taxonomist, but I think it leads to the need for a messy ontology layer to equate concepts from one publisher's corpus to another.
Andrew