It's not so much the size of the company as the number of data records I was thinking about.
My (small) company uses Peachtree Accounting. It doesn't have the function you're looking for, and I'm not sure if there are any off-the-shelf packages that do. But what almost all of them do
have are data export capabilities. Some also provide integrated or 3rd party report writers that allow for fairly complex reports to be generated from the underlying data.
By way of example, we need several work order analytical reports that Peachtree doesn't provide. We get around that by exporting the relevant raw data which we then import into a series of macro driven Excel spreadsheets. MS Office Excel and Word then generate all the nifty management reports we need. The entire process is now script driven and fairly easy to do. (Note: Peachtree also has 'bigger' and more capable accounting packages available. But they're fairly expensive and border on overkill for my organization so I can't comment on how well something like that would work for your company.)
Depending on the complexity of the reports, and the size of the data sets, our simple approach may or may not be viable for your company. However, if the accounting package you use has an SQL type database underneath it, you should be able to easily extract whatever you want and have some custom programs/scripts/reports written to meet your requirements.
If you go this route, the single most important criteria for selecting an accounting product would be the degree of 'granularity' in your data sets. Your accounting app would need to keep detail records of the data you need in its database. Not all accounting packages do. Some summarize and regularly purge detail records as part of a closing process or file maintenance procedure, so you'll have to ask the package's vendor just what data is tracked, at what level of detail, and how long it's retained.
Best bet is to do a mock-up of the report(s) you want and ask "Can your package do this?" And if not, "Can I get at the data needed to do it myself?"
Many accounting package vendors can arrange to provide a working demo of their product. Take advantage of that before you buy if they offer one. Also inquire into what training and support options are available. If you're going off manual accounting and onto a computer-based system for the first time, you'll want as much help, training, and support as you can get. It's a big job. Doable, but still a lot of work.
Hope this helps. Post any other questions or concerns here and I'll do my best to help you out.