When a web application wants to tell its user the size of the file the user intends to download, should the app tell the user its logical file size or the size of the file on disk?
I would separate the information. Tell the user the download size beside the link that actually downloads the file(s) and tell the user the size of the complete installation where the general information. If it's, for example, a software that needs installation - give that information in the Installation Requirements area (amount of hard drive space required, minimum amount of ram required, minimum CPU speed etc.)
This should give the user the size information in the correct contexts.
I believe it depends on the file the user wants to download.
I think if it's a file containing something the user has to install on their computer, I believe you should tell the user the size of the file on disk.
If it's a file, no matter how large, that doesn't need to be installed (like a movie, a music file or a document) I think file size is of more interest to the user.
Why? I'm not a tech-head but if I remembered correctly, a program that needs to be installed on the computer comes with more meta-data that needs to be stored on the computer so the difference between file-size and size-on-disk is larger than it is with other files. It is also a file that probably will be on the computer for a considered amount of time. Files like movies, documents or music files get relocated to external hard drives or send to other people after which they get deleted. Size-on-disk is therefor less important for the latter.
On an other note, the file-size is usually an indicator to me for the amount of time it will take me to download it. So in that sense I would be interested in both.