Hmm. I see a lot of steam-exclusive DRMy crap in this bundle (all though since when has humble bundle been anything other than this?) A couple of gems though:
Can't speak from experience, but I've actually heard some nice things about Stencyl and Spriter too. I'm not sure how much mileage you can get out of either one, but I know the dev for Ghost Song has a strong preference for Stencyl, and Spriter seems like a decent budget software for handling modular animations. With this bundle though, keep in mind that you're only getting a year license for Stencyl, and the Spriter version offered only activates on Steam.
Urho3D (an open source engine) has a 2D module that imports Spriter animation rigs, and its the animation format Klei used when they introduced modding support to Don't Starve. Spriter Pro would be worth the bundle alone if you could get the non-steam copy, but you should honestly never buy studio software on steam. Aside from the DRM being worse (the base version of Spriter Pro is just a serial number without activation if I recall), it treats it as a "game" and will be incompatible with any other tools you bought through steam (
see here for a reference to needing a workaround to run RPG Maker at the same time as something else.)
Urho3D and
Godot are both pretty nice engines if you're willing to script.
I bought Darkbasic when I was a kid. It was not very well built, and the same developers did the AppGameKit.
Sprite Lamp looks pretty cool!
The absolute best pixel art program, in my opinion, is
Pro Motion 6. It has amazing support for animations, painting across frames of animations, tileset painting (one mode lets you paint the tileset as though it was an image with an optional grid, which when "finished" is automatically chopped and de-duplicated across the grid to give you the tileset of whatever landscape you drew freely.)
Grafx2 is free but not quite as awesome, though still has a fair bit of awesome to it.
Engines wise, you can get awesome results with Unity 2d, the only problem is that you'll have to learn c (or it was C++?) which is a pain in the neck (specially compared to pyton or even ruby)
Unity traditionally uses C#, which is less of a pain in the arse than C++.