.FLV is a terrible format, on a lot of systems it gives a lot of trouble trying to run them locally. Remember, you want to make it as easy as possible for the customer, so a video should play by just double-clicking it. FLV doesn’t do that unless you have specific software installed.
As an embedding solution it’s fine….3 years ago, before iPhone/iPad got so big.
.MP4 is becoming more and more standard, plays fine on most systems so I would go with that too. Both Windows and Mac play that nowadays without the need for special software.
Other alternatives are .MOV and .AVI (DivX format).