You obviously recognise that every clip on YouTube etc will be subject to copyright in one way or another. The difference betwen producers like CBS and Joe Bloggs who makes a home movie and puts it up, is that the former will be more likely to take action over alleged infringement, whereas the amateur may well not care about protecting his copyright.
You didn't explain too fully what the purpose of your documentary was, but if you feel it could defined as reporting on current affairs, then you may be allowed to include clips of copyright works under the fair dealing rules contained in the Copyright, Designs and Patents Act 1988 s.30
There is no definition of current affairs in the act, but I would suggest that to qualify, the subject matter would need to be fairly newsworthy (ie what you might find in the news section of a newspaper) and not simply of cultural or historical interest. Also if you only use the minimum length of clip to illustrate your point, you are in a stronger position to qualify under the fair dealing rules. In a case involving a German television company called Pro Sieben and Carlton Television the Appeal Court found that the inclusion of a 30 second extract of a programme on multiple births made by Pro Sieben in a documerntary made for and broadcast by Carlton was fair dealing for the puropses s.30(2). In a separate case involving the review of a book written by L Ron Hubbard (of Scientiology fame) the judge Lord Denning MR said30. Criticism, Review and News Reporting.
(2) Fair dealing with a work (other than a photograph) for the purpose of reporting current events does not infringe any copyright in the work provided that (subject to subsection (3)) it is accompanied by a sufficient acknowledgement.
(3) No acknowledgement is required in connection with the reporting of current events by means of a sound recording, film or broadcast where this would be impossible for reasons of practicality or otherwise.
That said, obtaining clearances to use the clips need not be that difficult where you have details of the broadcaster etc. Here's a link to a useful BBC guide on the subject of clearances.To take long extracts and attach short comments may be unfair. But, short extracts and long comments may be fair.
Source: Hubbard v Vosper  2 Q.B. 84