I worked R & D at a big consumer packaged goods company and ran into a lot of these 'excel messes' especially dealing with raw materials specifications. Here are my suggestions:
The 'R' programming language is pretty useful for statistics and could be used to aggregate a lot of files (and its free). Also if you want to generate dynamic reports using templates then you should look into sweave which is a package in 'R'. (http://www.stat.uni-muenchen.de/~leisch/Sweave/) You could build beautiful PDF reports that you simply run a script to generate if they are easily created into a template. But that would also require learning Latex for creating documents, something that is used heavily in the academic world but I have yet to see it in the business world.
Another approach which I would try is to use a programming language to dump it into a relational database and then use SQL to access the info (which is heavily used in business setting). This option also also allows for others to use it with familiar business tools. My unconventional tools of choice would be Ruby and using Rails to build an interface.