You didn't include the original Sakura no Hanabiratachi PV either.
Not that I would have voted for it, but I would think it would be here for the sake of completeness.
1.
Sakura no Hanabiratachi '08 - It's not just a music video, it's a short film. And a very good one at that. The emotion conveyed through this PV really gets to me everytime I watch it.
2.
10nen Zakura - I guess I'm just a sucker for the storyline PVs. This one feels almost like a sequel to SNH '08. And though it's not quite as emotional, it does come very close.
3.
Keibetsu Shiteita Aijou - This song and PV deals with a very serious - and prevalent - issue. That final chord always makes my heart skip a beat, because I know what just supposedly happened. I wish they would do more of these serious PVs like this one and Seifuku.