I have an ajax spinner which unfortunately has a white background in the corners. I want to remove the white and make it transparent using GIMP. How can I go about doing that? I tried opening it in GIMP and changing all the pixels to red to target but that changed the whole image when I made red transparent, and also it didn't seem to perpetuate through the sequence.
GIF doesn't have "proper" transparency. You will always have to optimize it towards the intended background. And depending on the image you might have to change every single keyframe.
Note: Gimp does support transparency and then when you optimize for animated gif and export it will support transparency in the gif!
To edit a gif in Gimp, first open it.
Then look at the layers window (CTRL+L).
To easily edit an individual frame, uncheck the 'eyeball' for each frame that you wish to hide, then edit the remaining visible frame. (At this point you can edit in your transparency as needed, you may need to change color types if the gif you are opening loads without transparency support, but once it is there it will export properly with animated gif being transparent!)
After your desired edits are completed recheck all eyeballs so all frames are visible and then prepare for export by first optimizing via the filter menu: Filters -> Animation -> Optimize (for GIF)
This will create a new window with your optimized GIF, now just File -> Export and during the save make sure the 'Animated' checkbox is selected (other options such as framerate will also be available here).