http://my.smithmicro.com/win/anime/index.html
Anime Studio will do what you want but it costs $50, and then you'll have to learn the program, and then you'll have to create a workflow to export your characters and clean them up and import them as sprites etc, etc, etc. It'd probably be just as easy to slog through the process of animating things by hand in the long run.
Not to mention 2D character deformations tend to look a little funny and bendy at the joints. But it does things like paper doll animation too, I think.
You can use GIMP or something (or Photoshop or Flash if you have one of those) to fake the paper doll thing. Draw your body part in pieces (forearm, hand, foot, leg, whatev) then set those pieces aside. Then when you make a new frame, copy your pieces and rotate and place them where they need to go. Flatten your frames or take a screenshot or whatever, and then make the next frame.
Just a warning though... if you use a paper doll method to make animations, it will end up looking like you used a paper doll method to make your animations. In other words, not so good, unless that's the look you're going for. The reason those sprites that were made from a 3D model look good is because, well, they're 3D renders. If you have a program like Poser you can dress up a model and export some frames from the canned animations no prob (when shrunk down to sprite size, it's hard to tell it's Poser).
Really though, nothing beats putting in the time and effort when it comes to animation. I know it's tedious (it bores me to tears) but the only way to get quality work out of it is to put quality work into it. And that pretty much means tedium.