Lots of good answers here, so let me start at the top.
Looks like you are dealing with 3 issues/questions.
1. CMS - No difference
2. Shared server or different server - Google is most likely going to be able to determine an administrative relationship between your sites one way or another, so this probably doesn't matter anyway.
The real problem comes when you start to interlink 200 sites. This can cause penalty headaches when done aggressively between different domains or subdomains (especially in light of Penguin). This typically isn't a problem with internal links on the same domain. +1 for subfolders.
3. Subdomain, Folders, or Directories - As far as Google Places goes, all are fine - as long as each seperate business has it's own separate
- Webpage (whether it's on the same domain, subdomain or folder)
- Address
- Phone #
- etc
... then Google will treat them as different business that you can claim in Google Places. (and you can manage them in bulk)
The advantage of placing everything on the same (sub)domain is that you consolidate your ranking power. Instead of doing link building for 200 sites, you can link build for just one. (Although you still want to target local links to specific pages - helps a ton). As long as you spread link equity amoung the individual business pages (both internal and external) you may have an easier time ranking when everything is on the same domain. +1 for subfolders.
The disadvantage of the folder method is branding. It makes your URLs potentially longer, and you might prefer the shorter domain names for local websites.
There's no "right" solution, but if it were me, I'd build everything on the same domain.
By the way, here's an interesting article from Matt Cutts
"If you have a lot of store or franchise locations, consider it a best practice to 1) make a web page for each store that lists the store’s address, phone number, business hours, etc. and 2) make an HTML sitemap to point to those pages with regular HTML links, not a search form or POST requests."
Wish I would have found that before I wrote out my answer.