MP4 isn't a "format", it's just a container file that can contain any number of different codecs. These days it's most often associated with the H.264 Advanced Video Codec (AVC). VirtualDub has a freeware equivalent of that called X.264 and by default saves it into an AVI file, but it's functionally identical to H.264 within an MP4 file.
Thank you very much, but the Neat Video for VirtualDub filter does not work on VirtualDub2.
Make sure the architecture of Neat Video version matches to VirtualDub2 architecture, i.e. if you're using modern 64-bit version of Neat Video, then you have to use VirtualDub2 64-bit version too.