You have two options - force users to upload WCAG compliant content (which is near impossible, but you can improve things by insisting on alt text, .srv or similar format caption files for videos etc. and explaining why it is important) or you use a statement of partial compliance on the site, of which their are two versions.
Statement of Partial Conformance - Third Party Content
The W3C recognises that you cannot control third party content, including user uploaded and user linked (embedded) content.
Now here you do have two realistic options, depending on your available resources.
Option 1 - maintain the pages
If the content is uploaded to your website then you have the option to "repair" it. You can put a system in place to monitor newly added content and add / adjust the markup, alt attributes etc. to make the page compliant.
You would still add a statement of partial compliance but would also state that pages will get updated and maintained to provide full compliance within 2 business days.
Due to the heavy resource requirements on busy sites this may or may not be an option.
However this would be the preference if you are able to do this (to reduce costs you can combine this with any mediation / approval processes you have in place. For content that cannot be made accessible, for example your scenario of flashing content, you can have a simple warning box that can be used to explain the problems with the content.)
Option 2 - accept that user content is not compliant
A "statement of partial conformance" may be made that the page does not conform, but could conform if certain parts were removed.
You detail which pages / page types are not compliant, but explain which parts are compliant and which parts need to be removed in order to make the page compliant.
I would put a warning before any content that explains that it is user generated content and link this to your partial compliance statement. It could have a positive effect where a few people take the time to learn about accessibility.
