There's two types of VC titles: regular VC titles, and dedicated GBA VC titles.

Regular VC

Regular VC titles: an emulator application + VC ROM in the NCCH RomFS(among other things in the RomFS). The emulator build includes support for all supported VC platforms, not specific to just the included ROM platform.

This emulator includes GBA support, however the GBA emulation for this this is somewhat slow. This was presumably implemented before AGB_FIRM was.

Unlike Wii VC, the 3DS VC ROMs for NES use the "TNES" header.

RomFS

"rom:/rom/" This directory contains the ROM file(s). Filenames used under here don't matter: the filename is determined by the emulator app by doing a directory read.
"rom:/shaders/" This directory contains GPU shaders used by the emulator app: .shbin, .csdr, and .obj.
"rom:/VCM/" This directory contains graphics, audio, and text used by the emulator app.
"rom:/agb.bin" GBA BIOS.
"rom:/buildtime.txt" Emulator app build timestamp.
"rom:/config.ini" Emulator configuration .ini, contains sections for all supported 3DS VC platforms.
"rom:/<rom_name>.patch" rom_name = filename from the rom directory. This .ini contains patches for the ROM.
"rom:/shader.shbin" GPU shader.

Savedata

The savedata contains:

"rsm1.dat": Same format as the below rsm2.dat. Probably used for the "restore-point".
"rsm2.dat": Current emulator save-state, for storing/loading state at VC-title launch/exit.
"sav.dat": The actual savedata used by the emulated ROM.

Overwriting sav.dat with 0xFF-bytes doesn't have any affect on the actual emulator. Doing that with most of the rsm*.dat data doesn't crash anything.

GBA VC

GBA VC is run by AGB_FIRM. RomFS isn't used for GBA VC titles, but can be found empty within GBA VC titles. The NCCH ExeFS contains the same files as a normal application. The ExeFS:/.code contains the GBA VC ROM followed by a 0x360 byte long footer.

Footer

All values in the GBA VC footer are little-endian.

START	SIZE	DESCRIPTION
0x004	0x4	GBA ROM Filesize
0x008	0x4	Save type (see below)
0x020	0x1	Manufacturer info select (see below)
0x024	0x300	Unknown, three different types of this data have been observed.
0x338	0x4	GBA ROM Filesize
0x344	0x4	GBA ROM Filesize
0x350	0x4	Magic '.CAA'
0x35A	0x2	High two bytes of GBA ROM file size

Save types:

EEPROM (various sizes, IDs specified in footer): 0x2
SRAM/FRAM (128k): 0xE
Flash (512k): 0x9

Support for RTC and 1m-flash chips is not implemented in AGB_FIRM.

Manufacturer info: GBA games' SDK-provided save code only supports a range of manufacturers from which Nintendo was buying memory from around the time of that game's development. As such, most games don't support a generic emulated storage chip. This byte appears to select a manufacturer info set to emulate. This has been observed to be 0x90, 0xC0, and (in one EEPROM-based game), 0x80.

SRAM games up to and including V111 use 0xC0. Above use 0x90.
FRAM V103 uses 0xC0. V104+ don't exist, and lower versions also likely use 0xC0.
Flash V124 was observed 0x90, V131 was observed 0xC0.
EEPROM-based games vary wildly, since they can likely specify chip info in the 0x10-region of the footer.

NAND Savegame

AGB_FIRM saves its active save memory to NAND on exit, this is then immediately picked up by NATIVE_FIRM on reboot by checking CFG_BOOTENV. From there, this is verified and copied out to SD. The savegame format is as follows:

START	SIZE	DESCRIPTION
0x0	0x4	Magic ('.SAV')
0x4	0xC	Always 0xFF
0x10	0x10	AES-MAC of the SHA256 hash of 0x30..0x200 + the entire save itself, keyslot 0x24, keyY from process9 .rodata
0x20	0x10	Always 0xFF
0x30	0x40	Always 0x1
0x34	0x4	Number of times saved (unused?)
0x38	0x8	AGB TitleID
0x40	0x10	SD card CID from the console the save was made on (verified on load)
0x50	0x4	Save start addr (always 0x200)
0x54	0x4	Save size
0x58	0x8	Always 0xFF (?)
0x60	0x4	See here
0x64	0x4	See here
0x68	0x198	Always 0xFF

3DS Virtual Console

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