ext4 on all hard disks, but my installs are all several years old at this point, and I might choose differently if I were starting over from scratch. The boot partition on the ancient laptop might actually be ext2; I don't remember and it's certainly old enough that that might still have been preferred Gentoo procedure when I first set it up. Removable media might be ext3, ext4, or vfat, depending on compatibility needs and how long ago I formatted it. If I buy an SD card or USB stick that turns out to be preformatted in exFAT, I reformat it before use to ensure everything can read it.
They're all solidly reliable filesystems (well, except for the vfat), but perhaps not the most featureful.
Raw qemu at the command line for the one I use on a daily basis (not recommended for the average user). VirtualBox if I need to spin something up quickly but don't expect to need to keep it past the current testing cycle.