You should see the videos I think are crap (and thus don't favorite). Those were the cream of the crop as far as videos go. And you can narrow them even further.
Eh, those were the ones where I didn't think the music was too painful (or at least it was just really funny). And believe me, there are a lot of fanvids that are painful in ways I can't even finish (it also helps if the clip quality and editing is up to snuff). Perhaps to different people. Certain songs have me clicking away within seconds of opening a video.
I just use cheap-o Windows Movie Maker, which, as long as you don't use their titles (at least change the fonts and background color) and NONE of the horrible filters (they are a dead giveaway), shouldn't look too obvious. Most people use WMM, but there are some people with rather snazzy editing programs that do all those crazy things with zooms, cut-outs, overlays and colors.
An example of snazzy advanced programs vs. WMM:
Snazzy effects at an advanced level: http://www.youtube.com/watch?v=rYeAwrKqWAs
Mostly straight-forward, but a little more than just straight clips (use of blackouts and slight clip alteration--flipping, in this case--a good example of a "character study" video--also an example of a video that mixes music with unobtrusive dialog clips): http://www.youtube.com/watch?v=DfTDs44-n5c
WMM normal: http://www.youtube.com/watch?v=k4zzxkzcG4Y
(also a good example of comical song/clip association)
a good WMM edit job that needs to remove the DivX logo (a big no-no you have to learn how to disable in the DivX preferences): http://www.youtube.com/watch?v=gh_28msDuQc
And then there are the poor-quality footage, inept editing (either not enough cutting--you've got to severely chop anything conversational--or obtrusive video sounds) or picture videos which are bottom of the barrel.
You can kind of get an idea of what to do and not to do with videos from that. The best ones have some match between the lyrics and what's being shown on the video. The poor quality edit-jobs are often ones that reuse a limited amount of clips or don't edit fluidly and with enough of a selection of clips. And it's very tough to make a picture slide show even watchable.
I'm not particularly a fan of the non-canon rewriting/alternate universe-type fanvids. They just end up ticking me off because I'm familiar with where all the clips came from and their original contexts. A good example of that are a lot of "Sylaire" fanvids--the only ones I can stand are the ones that are honest about what their story is. Biased videos that are all about putting down one character are also a big turn-off (rampant in the Whedon fanbase in regards to Bangel vs. Spuffy or Angel vs. Spike).
An example of AU that I just can't get behind is Spock/Kirk. I've never been a slash fan.