Anyone want to suggest the best system for putting sprites on a sprite sheet?

Ways I can think of:

1) find the max width and height of any frame of a set of anims (e.g. the "jazz" set, the "bilsy" set, the "weapons" set..) and make a grid of cells that size.

or

2) place a sprite in the top left, gap of like a pixel, next sprite, repeat, until the width is filled, then start on next line down far enough that it won't touch the above sprites (i.e. a crude closest packed system..)


Other questions:
How much padding between sprites?
Should the sprites be centered in the imaginary cells, or aligned to top-left or whatever corner?
Should there be bounding boxes drawn around them?
What color background?
How wide should the sprite sheet be? A constant, or around the width to make the entire sheet close to a square?
Should I also export a txt file giving the coordinates of each sprite? What format would be useful to fangame programmers?

Last night I ripped close to all of the sprites I had (only the anims in the shareware version, I don't have access to the full version at school (I'll get my brother to send it to me from home though)).. (like 3500+) and it took around 20 seconds.. certainly makes the by hand ripping look slow.. ;p