When something is not included it is because it was not good enough for the band - it did not make it past the cutting room. Sometimes it was not included because it did not fit a certain theme the band wanted to convey.
Check out the B-sides of both the best of 1980-1990 and 1990-2000, you can obviously see that they are nothing even close in quality to the ones in the Best Of cd's that they accompany.
That's also one reason why I am not too hot on U2 releasing a boxed set of their unreleased material. My view is that if it were trash back in 1987, then it is still trash now and it would be against U2's principles to be selling to the fans work they don't believe in. As for the B-sides, they are not trash - after all they were released. But they will just forever be b-sides and footnotes and nowhere near as good as the actual songs in the album.
For that same reason, One Tree Hill did not quite make the cutting room in the Rattle and Hum vid.
Cheers,
J