I'm writing a basic sprite engine for my own amusement and to get better aquainted with Java's 2d API. Currently I am making use of large numbers of separate .png files with transparent backgrounds to represent the various sprites and different frames of animation that I need. Most 'real world' game development projects seem to make use of 'sprite sheets' which contain multiple sprites or frames of animation within a single file. Also, rather than making use of native image transparency support, people often nominate an arbitrary colour that does not appear in the sprite pallette to be the transparent colour. How does one manage a file like this programatically?
There may be other factors that I've not thought of here, so I may add to the list above as I think of things or as people make suggestions (please do so in the comments).
I currently use XML files generated by a simple sprite editor that store the sprite as a collection of (optionally animated) poses, which are in turn a collection of frames or cells. Frames store per-frame information like the x and y offset of the frame in sheet, cell width and height, and any transformation (resize/rotation/hue/etc.). Poses store individual frames and animation information (speed, for example), and a pose name to easily identify them in the program (hero.pose = sprite.pose["standing_right"]). Sprites serve as a document root to hold several poses, such as a pose for each facing direction.
A less flexible alternative I used earlier was to specify fixed sizes for cells and sheets and calculate frame offsets and sizes based on these values (e.g. width is always 32 pixels, so third sprite is at 32 * 2). Later I started specifying these dimensions in the file name (e.g. sprite_name_32x64.png) for sprites that don't fit the fixed cell dimensions. I like the new approach more, especially with a simplistic editor that fills most values for me and allows me to use sprites as templates for other sprites.
I use the alpha and transparency information stored in PNG images directly so I don't need to worry about storing it elsewhere, although other approaches would be to pick a fixed value per sprite and store somewhere, use the leftmost pixel in the pose if you know it's always empty, use a specific palette entry if you're using those, sprite masks, or what have you.