I wanted something very similar - except in my case, I am using my local cable company's multi-room solution for live television and DVR. But that can certainly be worked into a solution for you
I started with a NAS, and I'll let you know why: I wanted to have ALL of my content in one, central location. And from that one, central location, I wanted to be able to access ALL of my content from multiple devices simultaneously. That seems to be similar to what you want.
A NAS by itself is not a complete solution for you, however. But I DO think it is an important PART of what you want to accomplish.
I went with a Synology DS411j. It is a 4-bay unit that sells for around $300 (that's just the NAS enclosure, not any hard drives!). I put four 3TB hard drives into that DS411j NAS, giving me 12TB of hard disc storage. Each 3TB drive cost about $120. I went with Hitachi 5K3000 model drives. They are not the fastest drives in the world, but they are quiet, they run cool (always under 40 degree Celsius) and the DS411j is able to spin them down to save power and then spin them back up when you need to access them.
Synology's NAS units offer quite a lot of flexibility all on their own. Synology offers their own pseudo-operating system called the Synology Disc Station Manager. There are "apps" for the NAS so that you can access your files via the internet, set up the NAS to be a bittorrent client, set up the NAS to be an FTP server, set up the NAS to be an iTunes server, and several other functions. Basically, the NAS becomes your "one stop shop" for ALL of your media. You save everything to the NAS. From there, it is simply a matter of how you want to access your media. The NAS is NOT a playback device. Just a big storage tank!
I've connected my NAS to a dual band (2.4GHz &5GHz) Wireless-N router. I use the 5GHz channel for streaming all of my high def content around, leaving the 2.4GHz channel open for things like my Xbox360 and PS3 for gaming without interfering with the media streaming from the NAS.
You were also concerned with being able to control who can make changes to the files and access the content. Synology's NASes have you covered there as well. You can set a password on your "admin" account so that only you can have access to "admin" level control. You can then set up other user accounts. You can make those accounts "read only" if you like and they can have a password or not. For example, I have a "guest" account for visitors, which has no password and is read-only.
You can also set up your "shared folders". On your hard drives (which can be set up in various RAID configurations, as JBOD, or just as separate "basic" discs) you will set up "volumes". And then "shared folders" within those "volumes". You can designate a "volume" and any shared folders within it as "encrypted". You can also set up volumes that are not encrypted, but they are "invisible" to any file browser like Windows Explorer unless you type in the address to that volume manually. In other words, there are a variety of security measures available so that only you can access certain files and only you can make changes.
So now it becomes a question of how you want to access all of your content. The joy of the Synology NAS is that there are many, many ways!
In my case, I have made backup 1:1 ISO image files of my Blu-ray, HD-DVD and DVD collection. Because I have chosen 1:1 ISO image files, playing them back is not so easy. The Popcorn hour is about the only stand-alone device that is equiped to play ISO image files, but given its price and its sometimes "buggy" nature and rather plain-looking interface, I decided to go a different route.
I went with a Windows 7 HTPC. For me, it is the best solution. Windows 7 Home Premium or higher comes with Windows Media Center baked in. And it is a slick-looking interface that can be controlled with a normal IR remote control (like a Harmony, for example).
There is a FREE program called Media Browser that works inside WMC to give you an even better, even more flexible interface. You can also install various codec packs so that WMC can play back almost any file type. In my case, I'm "mounting" ISO image files, so WMC just "thinks" that I've inserted a physical disc. That requires Blu-ray and HD-DVD playback software. In my case, I use TotalMedia Theatre 5, which costs $99, but works beautifully.
Now, you might not be worried about physical Blu-ray discs or 1:1 ISO image files. You're probably more concerned with MKV files. But you also wanted to do things like encode or transcode files. And because of that, I believe that a Windows 7 HTPC is your best solution too.
With WMC, you can also install multiple TV tuners and use your HTPC as a very slick DVR. With DVRMStoolbox, you can automatically remove commercials and adjust your recording schedule to your heart's content!
With the new "Sandybridge" Core processors from Intel, you don't even need a separate video card for any of this. In your case, since you're worried about speed and transcoding and whatnot, I would recommend that you go with a Core i5 Socket LGA1155 CPU. While the Core i3 Sandybridge processors are more than ample for almost any HTPC, your desire to run multiple other programs while also playing back content makes the i5 a better choice, IMO. There is a "low power" version of the Core i5 called the Core i5-2400S. But you can get similar power savings and actually slightly better performance by using the regular Core i5-2400 and simply lowering the CPU voltage on your motherboard in the BIOS setup. Regardless, it's a remarkably powerful processor. And with a matching motherboard, you get full 1080p video output via HDMI - even FullHD 3D support! You also get full HD-Audio bitstream output support over HDMI, or you can decode the audio with the HTPC and use analogue audio outputs to self-powered speakers if you really don't want to use an A/V Receiver.
Given that you want multiple TV tuners, you will probably want a micro-ATX form factor. I went with the even smaller mini-ITX case, but that only leaves you one, lone PCIe slot for a TV tuner card.
So that's going to be your main "powerhouse" unit. You combine the Windows 7 HTPC with a NAS and you can pretty much make any file type you want and store it all on the NAS so that other devices can access it through your wireless network or over the internet. You can off-load bittorrent download duties to the NAS. The Synology NAS can also serve as a DLNA 1.5 server so that a PS3, Xbox360 or any media streaming device can access compatible file types via DLNA from the NAS.
With the NAS being able to feed ALL of your content to any device that you have, you won't need to keep your HTPC running all the time. Just the NAS can stay powered on 24/7. You would only need to wake up the HTPC when you want to use it for playback or when you are running a transcoding task or some other regular PC duty.
You don't HAVE to use a NAS. You COULD just put a whole bunch of storage into your Windows 7 HTPC and use it as a DLNA server too. But I personally think that the NAS solution makes more sense and is more convenient. In my case, I actually have two DS411j units, each with four 3TB hard drives installed for a total of 24TB of network storage space, plus I've got four 2TB external USB drives that I can connect to the DS411j units for up to 32TB of space. I have all of that storage because 1:1 Blu-ray backups are HUGE - about 40GB a piece! So I eat through storage space VERY quickly
Anywho, for everything that you want to do, a Windows 7 HTPC makes the most sense, IMO. You can build one for surprisingly little money. Combine that with a Synology NAS and I believe you could accomplish everything that you want
