I have a feeling I should know what you're talking about, but it's been years since I played MMBN 3, and I don't feel like completing the god damn crane puzzle thing at the very end.
I do know that Marisa's chip folder would most likely comprise of powerful chips, and she uses them without care for strategy or skill.
I'll give you one hint: Why was the virus combination for the 2nd part of the Scuttlest Family so utterly aggrivating if you weren't fast enough? I mean, getting caught is the small part . . .
As for Marisa's folder, I can guarantee you it'd probably have Cannon chips, TankCan chips if it's post-BN5, and Cannonball most definitely. And that her NaviChip would HURT.
Reimu's, on the other hand, would be homing. Whether she's Target-type or not (or pre-BN4), it'll home. Definitely.
EDIT: This is starting to get me to seriously consider drafting folders for Touhou characters. Whether or not they'll be MMBN3 or MMBN5 (the two games I liked best) will depend on whether or not I can find a ROM to replace my missing Colonel cartridge. As it stands, White Version is hanging around somewhere in my house and I'm wondering if Cirno would be nearly as annoying as Bubbleman to fight in MMBN.