What file formats should I use for maps?

Question

I've come to the IL forum simply because of the number of file formats IL will process.  My question however is more generic to file formats.
I work with a large local county government (just as a citizen) and one of the projects we're working on is to get a full suite of maps (and other GIS output) for distribution.  Although they will be made available online, the intent is to print/plot.
For some maps, we'll want to have the capability to add vector graphics (ovals, rectangles, text, arrows) for highlighting.
The intent is for the county to provide machine readable GIS output so that we can do our own printing (via Kinkos for example).  We'll also be putting the maps online although only for simple viewing and downloads.
What file format(s) should I ask to have the map sets in?
Because I'm a novice when it comes to understand which format to ask for I've done some homework on jpg, tiff, gif, etc.  I think IL will take in any of them and that's where any vector graphics would be added (for print destined output).  I also have FW which could be used for web destined output if needed.
What is most important is the quality of the printed output so I'm assuming dpi is going to be important.  I'm also assuming that we'll ask for the output to be intended for a rather large plot (e.g. 36" x 48" or perhaps even larger) even though we may not actually produce a map of that size.  For what I've learned on this and other Adobe forums, no matter what file size and format we get, printing to larger paper will eventually lose visible resolution thus the intent to start with the largest we'd ever print.  We might have circumstances where we would crop but again understand what can happen when blowing those up.
One option, of course, is to have the county produce PDFs.  Is that a good idea for our purpose meaning do we lose anything to have the file format generally acceptable?  I'm assuming somewhere along the process we'll need to produce pdfs for downloads but that may not be the best format to get from the GIS output.
Keep in mind that we don't have GIS software at present.  In the future we may move to using a GIS viewer which would mean we would have file generation capabilities, but for now, we're going to have to handle non-gis output files.
I'm not even sure I'm asking the question well so feel free to educate me along the way.  I'm interested in learning.
Tom

Answer 1

(pricy)  I know that may sound strange given having CS2,
Yep. Sure does. Plus:
So in comparing prices, be sure to include the costs of the third-party plug-in route, such as MAPublisher (and the associated headaches of mission-critical dependence upon third-party add-ons in general).
Since IL can take in pdfs and can add vector markup
Working with PDFs is pretty much universal these days, for practical purposes.
Understand this about PDFs and Illustrator: Illustrator's Save As...PDF dialog provides an option for "Preserve Illustrator Editing Capabilities." Selecting that option actually embeds in the resulting file a full duplication of the file as native Illustrator objects. That results in very bloated PDF file sizes--because they contain two full copies of the file.
That's not what you want to do for PDFs that will be distributed/downloaded. So you're going to want to keep your AI-native files separate anyway. Opening a PDF that was saved without that option turned on in Illustrator is pretty much the same thing as opening it other mainstream drawing progams. So the "seamlessness" of PDF/Illustrator is really much about marketing.
But no matter. Your mind is already made up to use AI for this. If it were me, I'd be exploring all options.
JET