Leroux: From my experience, while GOG gives you an installer, Humble provides .zip files instead. Sometimes they contain an installer as well, but I think most of the times they just contain the games' folder ready to be unpacked. Meaning there probably won't be a proper installation with changing of registry entries, the folder is portable, and if you want to remove the game from your harddrive, you have to delete the folder manually, it won't be listed as installed program in the Control Panel. Whether that's a pro or a con or neither is up to you to decide.
Zip files can be opened and unzipped/extracted using any OS?
Portable folders don't mess or clutter registry?
The installation time is how long unzipping takes and unistallation time is how long it takes to hit the delete key?
These are definetely pro's and should be rather standards than exceptions in software distribution.
Of course, Humble doesn't have any standard in the distribution.
You can have zip files sometimes, sure. Then again you can have rar's or something else. And of course exe's too. Or sometimes exe's inside zip files. Or some more uncommon file formats, like Flash-based games or whatever.
I actually wish they would have zip's (or rar's) for all of their games, which would be consistent and you would know for sure what you are going to get.
And to answer the original question, the difference between GOG and Humble
Bundle is that GOG is selling games 24/7, whereas Humble has bundles which appear every now and then, contain a random selection of games which are sold only for a limited time never to appear in the same bundle again.
The "real" Humble Bundles have been always DRM-free, but Humble also sells other kinds of bundles, which may only contain Steam keys or have only few games as DRM-free downloads. Reading the bundle description will tell you what you are paying for. Usually you can choose how much you pay for the bundles as well, although some tier levels have minimum prices and if you want to have Steam keys you need to pay at least one dollar.
Of course, buying from Humble
Store is a different story, but the question seemed to be about bundles.