To configure FFmpeg for iOS:

./configure --enable-cross-compile --arch=arm --target-os=darwin --cc='clang -arch armv7' --sysroot=$(xcrun --sdk iphoneos --show-sdk-path) --cpu=cortex-a8 --enable-pic

If deploying to all generations, it's recommended to do separate out-of-tree
builds for each architecture, then lipo together the resulting libs. For
instance, assuming separate builds in armv6 and armv7:

lipo -create -arch armv6 armv6/libavcodec/libavcodec.a -arch armv7 armv7/libavcodec/libavcodec.a -output universal/libavcodec.a

and similar for each library. Then in XCode, make sure to build for both armv6
and armv7. If you only care about one generation (since the armv6 devices are
too slow for instance), then lipo is unnecessary of course.