The Official M&L3 Ripping Project *WARNING CONTAINS SPOILERS*

[Ridge Troopa]

Personally, I'd ditch the shadows. I'm sure the "pure" sprites don't have shadows attached.

You and Puggsoy are both correct when you say that shadows dynamically resize and are drawn separately. While this is true, they are still necessary as an animating tool/guide.

For one thing, it's pretty inconsistent to ditch shadows now when almost every other sheet on the archive has been ripped with shadows.
For another, I don't see how it's a benefit to get rid of them. You literally cannot animate properly without using them as a guide to place frames in a bounding box. Trust me, it's incredibly aggravating when you try animating Mario, Bowser, or any enemy without shadows as he'll just spaz all over the damn place. While it is entirely true that people will use these sprites as they see fit, it's still extremely helpful and looks nice when shadows are included.
As one who has worked with this style and its mechanics for years, I can assure you that it's better not to erase shadows. During idle and walking animations, for example, sprites can and will shift horizontally from the shadow sometimes. Leaving the shadow there indicates the movement of the character, as the shadow itself is always static unless there is actual translation of the character across the screen.

Why do you think I'm bothering to rip Bowser's overworld in bounding boxes? And not battle? Shadows.

Puggsoy, I don't know if you're doing this, but you can disable layers in DeSmuMe. This will leave your shadow one color and it's easy to capture. As for jumping, you can look at any sheet with jumping or flying poses on the archive.
EDIT: Right, you also asked about arranging animations. For things like battle idles, it's better to make a full loop so there isn't any confusion as to how it animates. If you need to indicate how a 'quirk' (when Mario stands taller and raises his front arm in his idle, for example) fits in, just add a small note saying what frames to replace every x loop.
EDIT 2: As an example, here's what I have ripped. Feel free to use or whatever if you want, I never planned to finish.

Ridge's small Mario battle rip

Partners in Time shadows are the same deal. Jumping shadows were different in that style, though (they get bigger and alpha out as real shadows do) but in BIS the cartoon approach of the shadow getting smaller is used.