When I first starting using D4, I saw many issues regarding clean urls and recommendations not to go there just yet in Drupal. So I didn't. Now that I am in D6 and clean urls shouldn't be an issue, I switched.
I didn't switch until I understood that clean URLs are similar to aliases. Meaning, if some other web site was linked to one of my unclean URLs, that link would still work. I must have read a dozen posts on DO looking for this answer. So I did a little testing and tada, everything is okay.
Clean URLs and Views
When I switched on clean URLs and tried to create or update a view using Views 2.4, the view features that let you set up the parameters of the view didn't work. You can see the error below. For now, I am toggling between clean and unclean URLs when I need to create a view. UPDATE: I don't know exactly how it happened but this issue has solved itself. See http://drupal.org/node/427542#comment-1494620 for more details.
Clean URLs and book outline
When I switched on clean URLs and tried to use the node book/outline feature, I get this error. The issue with views has been resolved but the book outline has not. So whatever fixed the views issue is not the cause of the book outline issue. See issue http://drupal.org/node/428792