I decided to give trying to hack the save file of Pokemon Mystery Dungeon: Explorers of Sky, and have had more success than before.
The save file is 128KB. The first and second 50KB segments are exactly the same, probably to ensure there is no error. If you try to change one of the segments without fixing the checksum, nothing happens. If you apply the same change to both, the game thinks it is corrupt and deletes it.
I'm not sure of what the third segment of the remaining 28KB is for, and the game seems to run fine if you delete it.
In the 1st and 2nd segment, there are two areas that are always different. Seriously, I change my team name, then change it back, and they are different all three times. I think that one is some random/other value that we'll never know, and the other is a checksum that includes that.
0x0000-0x0004 - not a standard CRC-32 containing 0x30-0x31.
0x0030-0x0031 - not a standard CRC-16 CCITT. My bruteforcer did not turn up any results containing the team name, which I know for a fact is in some checksum.
Also, some locations I've found:
0x990C-0x990F - Held Money. You must left shift the bits two times, and get the UInt16 from the second and third bytes.
0x9915-0x9916 - Stored Money
0x994D-0x9957 - Team Name. ASCII for regular English characters. I haven't tested other characters.
0x9960-0x9961 - Probably part of play time. Changes every time I actually load the save file, but not when I for instance change the team name.
I have attached a program (Truncated to Explorers of Sky .exe) that will split a save file of this game into its 3 parts (not recombine though). Should be self-explanatory.
[update] Checksum found, and save editor released.
http://projectpokemon.org/forums/showthread.php?29465-Introducing-the-first-save-editor-for-Mystery-Dungeon-Explorers-of-Sky
Any updates on research should be posted in that thread.
Explorers of Sky .exe
Sky Viewer..zip