Most CMS systems that are widely distributed by sources like PHPNuke, PostNuke, YaWPS, XOOPS, are PHP based. I have personally worked with all of them and had no trouble getting an "index.php" page optimized and in top position. However Apache mod rewrite can be used ofr all of the above. As well most of the above systems support Microsoft servers. re-write is another issue but a good windows based web host should have a solution for you.
See a full list of CMS systems here:
http://www.opensourcecms.com/
The trouble comes in when you want other pages listed. Google (in my opinion) still does have MAJOR issues with indexing dynamic URL's. I have seen Googlebot hit dynamic pages repeatedly in attempts to read past the "?" and not be able to make it through. This is NOT a selective problem or a problem generated by webmasters who accidently "restrict" access to forums for example.
On good option is a PERL based CMS. Engines should have no problem reading these. See Slash Code:
http://slashcode.com/
Hope this helps!