I have worked with several animation programs so I think I can give some imput over this.
Spriter: Skeletal animation tool. I believed a lot on this one, even backed the kickstarter, but after months of development with very little progress I have to say that spriter amounts to "you get what you pay for".
I'm currently working with Spriter, but only because I started with it and switching tools at this point would mean undoing weeks of work, but this is the first and last time I use it. The program is unstable, prone to crashing or freezing, and it has several kinks in its workflow that are not intuitive in the least.
The only pros I can think for Spriter is its construct integration, that there is a free version that comes with almost everything the Pro version has and that the Pro version costs $20.
Spine: Skeletal animation. This one is rather funny, they started development because spriter was taking too long, it was supposed to be a simpler version of spriter, with less features and such, but it had a much more steady development and right now it's leaps and bounds ahead of spriter.
The files Spine creates can be imported directly on GameMaker and GMs got functions to deal with Spine's skeleton, and also there's a very good Unity integration module flying around their forum I think (there are more I think), the standard version is $60, but I would recommend it over Spriter pro any day, and the pro version ($300) has a full featured free form deformation tool (this is what vanillaware uses to make its characters, there is a nice example of spine doing it in its forum, in the showcase section, a thread called "2 girls animation").
Flash: The animation classic, still one of the most powerful animation tools out there. Vector animations can be imported directly into game maker, as long as they don't use movie clips. Bone skinning is available and very good if used properly.
Cons: Really expensive unless going for yohoho version.
After Effects: Great for skeletal animation with freeform deformation, but again, very expensive and it's not very flexible regarding making animation for games. Still, it's unbeatable when it comes to animating special effects like sparks and explosions.
Photoshop: Get outta here, now. Only good for small, frame by frame animations. Also, if you don't have a wacom tablet, you will have to go another drawing program to clean your drawings (photoshop, unlike sai or painter or manga studio, has no trace smoothing, wacom tablets do the smoothing via driver, that's why your lines are crap if you are working with another brand of tablet and photoshop).
Anime Studio: Mostly skeletal animation. Rather cheap, but again, you get what you pay for. I only worked on a couple projects with this one, and it was riddled with weird bugs and I had to constantly revert to back ups because files would get corrupted or bugged to the point they couldn't be worked on, this was years ago so they could have fixed the bugs, yet this is smithmicro we are talking about, so I don't think so.
Animations you make with this can only be rendered as images and used as regular sprites, so usability for games is rather limited.
Toon Boom: Best 2D animation tool out there, most expensive 2D animation tool out there. Again, animations will need to be rendered as images to be used.
Flipbook Pro: To me, ridiculously expensive for what it does, it's the best frame by frame animation tool, but having to pay hundreds of dollars just to be able to use layers and go beyond 800x600 makes this tool a hell no purchase for me.
Pro Motion: Pixel art animation tool. Never personally used this one, since I have never done pixel animation, however I hear it's the weapon of choice for most pixel animators.
Anyway, if you want to take my word for it, if I would have to recommend an animation tool for making games, without a shadow of a doubt I would say to get Spine.
