On this page you will find all the BattleChip drop rates in the Mega Man Battle Network series. All of them were extracted from the North American versions of the games. The tables can be found below. You may notice several enemies are listed that cannot be encountered, or never drop anything. This is because all enemy slots, even unused ones, have reward data. The unused data has been left in for those who are interested.
In all games, your Busting LV. affects which drop you get. From Battle Network 2 onwards, the drop you get also depends on how much HP you have left at the end of the battle. This is a percentage of your maximum HP (including boosts from the Navi Customizer).
In Battle Network 3, under certain circumstances you can gain a higher Busting LV. than S. They will show as LV. S on the results screen, but internally the level is higher. I've labeled these ranks LV. S+ and LV. S++ in the drop tables. Apparently the GameFAQs community calls them Off-Color Custom Rank and Custom Rank respectively, or Team Rank collectively. There are only two ways to get these:
Download the tables below. All of them are encoded in UTF-8, so you might need to change your encoding to get it to display properly.