The following table should contain all the file formats FFmpeg currently supports, along with audio/video codecs each format supports. The table should help distinguish which codecs can be put inside which formats.

The columns are the following:
Format name - The formal name of the format.
FFmpeg format - The name of the format as used by FFmpeg tool. The list of all supported formats can be viewed using "ffmpeg -formats"
Codec name - The formal name of the codec.
FFmpeg codec - The name of the codec (enCODer/DECoder) as used by FFmpeg tool. The list of all supported codecs can be viewed using "ffmpeg -codecs"
Comment - A free form text comment.

Video

Format name	FFmpeg format	Codec name	FFmpeg codec	Comment
FLV	flv	GIF	gif	GIF (Graphics Interchange Format) image
FLV	flv	PNG	png	PNG (Portable Network Graphics) image
FLV	flv	JPEG	mjpeg / libopenjpeg	JPEG / JPG still image
FLV	flv	H.264	h264 / libx264	H.264 video encoder (libx264) and decoder (h264)
FLV	flv	VP6	libvpx ?	libvpx is used to encode VP8 video, but not sure about VP6 (need correction)

Audio

Format name	FFmpeg format	Codec name	FFmpeg codec	Comment
FLV	flv	MP3	mp3 / libmp3lame	MP3 audio encoder (libmp3lame) and decoder (mp3)
FLV	flv	AAC	aac / libvo-aacenc / libaacplus	FFmpeg's internal aac encoder/decoder (experimental), external library libvo-aacenc is used to encode AAC-LC audio and libaacplus library is used to encode  HE-AAC v2 audio known as AAC+

References

FLV format:  http://download.macromedia.com/f4v/video_file_format_spec_v10_1.pdf