First off, don't do it. Seriously, don't.
You are going to take ownership of a few hundred processes that not only are not your job, they aren't your specialty either. More so, you won't do it right ( trust me ) and you will be creating a full time job ( or 6! ) fixing and maintaining a system that never works right.
If you are in an environment that can generate such a large business process, I hope you are in an environment where you can get reasonable funding. What you want to look into is BPM software, meaning Business Process Management. Companies like Captaris, K2 and Ultimus all develop products, as do big boys like IBM and the like. These tools allow you to give the tools to business experts, so the people in the process that actually know what they are doing, then you have domain experts controlling their own domains, generally in a very excel like environment, but sometimes using tools that look alot like Visio ( or.. that are visio! ). You as a developer then, provide the transport between departments, and specialized logic to tie your various business systems together ( or to pull data from various sources.
Granted, BPM software start in about the 20K range, and the sky is the limit from there. Plus, as you expand you will probably want a document repository like Sharepoint ( which can start from as low as free and up to 100K+$ ) and a forms system like Adobe or Infopath, but all told, you can build a scalable end to end system starting around 30 - 40 grand, depending on the number of users you have.
That might sound like an obscene amount, but truly it isn't. Factor in you labour costs, all the labour costs of the various people you will have to meet with, the fact your are probably creating a full time job for a few people and creating a system that probably will never really be 100%... the money is well spent.
Keep domain specific knowledge in the knowledge experts hands, and keep IT specific tasks in IT's hands. This is an area where I see IT department after department screw up and end up with highly valuable employees getting paid high salaries to baby sit report generation. Honestly, I say again, don't do it! This is one of those areas where off the shelf products will be vastly superior than anything you can create.
(Note, most of my examples betray my most recent background. I am from a Windows shop with a .Net centric development team. You can just as easily find BPM solutions for Unix, Linux, whatever, including a few open source options with Java as the back end instead. )
EDIT: Oh, and for the record, if you absolutely can't buy off the shelf, if your budget is zero $, you will find most commercial BPMs implement a state based machine, with a gated flow chart-eqsue structure with a database ( or even spreadsheet ) driven back end. If you need to do it yourself, you would still be well served trying a demo from any of the various BPM providers and emulating their approach.
EDIT2: Links.
Captaris
Ultimus
Open Source (ProcessMaker)
There are tons more, but these will get you started. BPM software is one of those things that can go from thousands to millions of dollars, and potentially free. I can only speak towards Captaris, which I choose about 3 years ago and worked as advertised.