My thoughts on the list:
1. I've never watched Dollhouse, and I probably never will, so I won't comment on their inclusion other than to say they feel forced into the list simply out of the need to have something from all the Joss shows.
2. On the same page, I've never watched Firefly (save for the movie, which I own), but I am fine with the ones listed here as these are the ones that are constantly brought up to me by friends.
3. The treatment of Angel on the list totally baffles me. All of it. Five episodes (which sounds about right, I suppose) of which, four of them are from Season Five?! HUH?!! I can forgive the inclusion of the shippers wet dream "I Will Remember You", if only because it sets the tone of Angel having to be willing to give up happiness on any level to really redeem himself, but to not include anything from Seasons 2-4? Ludicrous. Anything that purports to be the Best of Whedon including Angel and doesn't contain mention of either the Angelus arc of Season 4 or the misanthropic dark Angel arc from Season 2 isn't worth the web space it's written on.
4. I'm fine with the absence of Becoming because the list still includes both Passion and Innocence. If you are going to sum up the Season 2 Buffy/Angel arc, then those episodes work just fine without including Becoming, which contains the "Buffy leaves town" segment that only hampers everything else.
5. I'd have put Restless higher, but that's just me. There was real art involved in that one, and I still think it represents the pinnacle of Joss' writing. Is it really that difficult to write about teen angst in regards to sex (like Innocence) as compared to pulling off surrealism in what is ostensibly a teen drama show? I don't think so.