Good eye on TDI: it's definitely flash.
Storm Hawks (which I've only seen a couple eps of) is 3D CGI with a color palette that makes the characters appear cel shaded.
When Samurai Jack debuted at Comic-Con, it seems like Genndy Tartakovsky said it was a mix of traditional and computer animation. It's been a while since I watched it, but if memory serves there were some elements rendered entirely in 3D with cel shading to match the 2D animation and backgrounds. And while some animation in the show resembles flash quality, the action and movement are generally quite fluid and doesn't have the stiffness that normally plagues flash animation.
Not familliar with Skyland, but a quick look on the ol' u-toob tells me it's 3D with a lot of mo-cap and cel shading in the character animation. Cool-looking show -- I'll have to see if it's available to rent.