Here's something handy to know that I had a bit of trouble finding information on. Perhaps I didn't look very well, but I was working with a colleague who had created a ClickOnce app and was having an issue where it appeared some of the files weren't being updated properly when he published a new version. Well, the problem turned out to be something else, but we were still curious on where the actual files were being downloaded to. After some digging, we found them at
C:\Documents and Settings\Jason Lautzenheiser\Local Settings\Apps\2.0
Under that folder are two more folders one called DATA and the other with what appears to be a random name. Under randomly named one, two levels deep are the main folders where all the different smart clients are downloaded to. It appears that each smart client will keep two versions, the current one and the previous version. I'm assuming this is for easy rollback a version.
Under the DATA directory any application files that the Publish Status is set to DATA.
Maybe this is well known, but it doesn't appear to be well documented.