Linux: How to determine the best filesystem format

First and foremost, this is going to depend solely on your architecture, and customs.

I for instance mount things like this under /mnt. I know people that create top level directories, and people who put this stuff in /home. It all depends on what you're comfortable with. There is no distinct standard on this anymore, the architecture of the system has changed, and you have varying views now, on things that used to be 'gospel'. Things like /usr/local or /opt/share, rpm or source...you get the drift.

Secondly, if you re-read through your link at pathname.com, you'll notice the paragraph under /media that states

Rationale

Historically there have been a number of other different places used to mount removeable media such as /cdrom, /mnt or /mnt/cdrom. Placing the mount points for all removeable media directly in the root directory would potentially result in a large number of extra directories in /. Although the use of subdirectories in /mnt as a mount point has recently been common, it conflicts with a much older tradition of using /mnt directly as a temporary mount point.

So personally, I advocate /mnt/windows or some iteration of that. It keeps the top level dir free, and is simple and intuitive. When I'm looking through or auditing a system, that's where I look for mounts right off the bat.

There's an EXE installer for Puppy Linux which boots from an .iso on FAT32, NTFS or Linux filesystems (i.e. ext2/ext3/ext4, xfs, etc.) using syslinux and runs in RAM using unionfs/aufs with full access to persistent storage (disk, SD, flashdrive, etc.).

Other ISOs can be mounted, from commandline or script of course, as well as by clicking on them in the included ROX-Filer file manager. One convenient use of this is to selectively access or restore files from an old version instead of having to roll back everything.

The original Puppy Linux distribution ISO, which itself is an usually an ext3/4 filesystem, is kept on the lowest layer of the aufs stack. Changes are recorded in the topmost layer and flushed to disk periodically (configurable) to a "savefile". On boot, the original ISO is loaded to RAM and mounted read-only, then the savefile is loaded and mounted read-only to overlay it and an empty read-write layer mounted for any new changes. To preserve a history of changes, just setup automatic or manual coping of the savefile ISO to an archival directory.

The O/S "layering" of unionfs/aufs along with multi-mounting of filesystems are the core technologies at work here, so if Puppy Linux doesn't work for you, look for other distros using them.

There are quite a number of installation options available for Puppy Linux including a Windows EXE Installer which is a separate package that sets up the Windows boot loader for dual-boot.