1. S-off/on are the terms used to tell if the security feature that prevents you from rooting is on or off. This is found under your bootloader, or hboot. To check and see if your device is s-off or s-on simply turn the device off, hold down the vol - button and turn the device back on while holding it. That will bring up your bootloader (hboot) and will show you what version it is as well as if your device has security on or off.
2. Rooting/Perma-Rooting are basically the same thing. Perma just stands for permanent. Rooting is gaining SuperUser (Admin) permissions for your device.
3. ClockWorkMod is a custom recovery tool that replaces the stock recovery tool in your bootloader. It allows you to flash(install) new roms.
Just expanding a bit, as I understand the terms:
1. With S-On, there is a security check on the signature of a ROM, before it is allowed to be flashed. It also protects the NAND flash memory, where the ROM is stored. Basically, with S-Off, you can flash just about any ROM meant for the device, including user-made "custom" ROMs. With S-Off, you can only flash "official" ROMs.
While related to root, they are not always co-dependent. On some devices, its possible to root, but still have S-On. You have SuperUser access (at least most things), but you can't flash custom ROMs. With root plus S-Off, you have access to just about everything.
HTC is constantly changing their security, so for the Flyer, it seems that S-Off was instrumental in achieving permanent root.
2) Rooting an Android device gives you "root" or "super user" access to system files, which are normally protected. There are a variety of things this allows you to do. You can change system fonts, and make other theme customizations. You may be able to overclock the CPU (depending on the device and kernal) or make other performance enhancements. You can remove system apps (like bloatware) that you don't need. Some apps require root to work, such as Titanium Backup and Clockworkmod for creating backups of app data or your entire ROM.
One thing to remember, is that the system files are normally protected for a reason. Don't modify or change anything, unless you have a good understanding what you are doing, otherwise you can really mess up your device.
The distinction between rooting (or perma-root) and temp rooting is made, due to the increased security HTC has applied to the NAND flash memory on their more recent devices. Basically the NAND protection means that a temp root will be wiped out when the device is rebooted. But some root functions can still be accessed during the temp root. But it also means you have to temp root every time you want super user access (if the phone was restarted since your last temp root).
Once the NAND protection on the Flyer was bypassed, it made a perm root possible. But on other devices, I know some users actually prefer temp root over perm root. You still have access to super user privileges while temp rooted. But if something goes wrong with your phone, its less risky, as a reboot will wipe any trace of the temp root (technically, rooting voids HTC's warranty . . . but its often possible to unroot for warranty purposes).
3. Clockworkmod will also make a full backup of your entire ROM (including user data) , so you can return to it any time. Handy if you have some catastrophic failure, or just want to switch back to the current ROM.
