How do pages that are created/managed by content management systems fare with SE's?

I have never used one before because I am aware that any "?" or other symbol in the URL of pages would hurt ranking; however, I have over 100 sites that are related and it is becoming a management nightmare.

I have a sign business and I am writing separate sites for each product and each keyword/phrase of each product. It is working well as far as ranking very well with search engines; however, I am very tempted to try a content management system to keep them organized.

Is this a route you would persue and is there a content management system you would recommend or would you stay with the separate HTML pages/sites?