Personally, I still just use youtube-dl for youtube videos; as an added bonus, I also never have to deal with choppy video due to poor streaming. youtube-dl -b -t '<paste youtube URL here>' downloads a video, or a whole playlist. "get-flash-videos" works surprisingly well for most other sites, as do various bookmarklets for sites that dig out the video URLs. Apart from video of various kinds, I almost never run into flash content I care about; the few times I have, I either try gnash (which works fairly often), try another site, or just not bother at all.
I don't find it particularly problematic to not have Flash on my system. I don't claim that everyone will find it as unnecessary as I do, just that I manage to do without it and not miss it.
I do, however, look forward to WebM more-or-less eliminating the need for Flash on video sites in the not-too-distant future, hopefully making it increasingly difficult for other sites to count on Flash.