I think you'll find that storage is mutable, sandtrooper, what you do will change as your requirements and needs change, and you'll only figure out those needs and requirements once you get up and live with your new system...and start making mistakes, like not properly backing up your system or your media. Speaking as someone who has used Thunderbolt ever since the 2011 Mini was released with it, I can tell you that you'll have a hard time reconciling this:
I'm also considering this Thunderbolt dock and then adding USB 3.0 drives to that
I would like to keep this project as cheap as possible though
If that product ever shows up, it will cost as much as or more than your Mini itself. If you felt you really needed some USB 3 expansion opportunities, you're better off selling the 2011 and picking up a refurb 2012 Mini, which has it built-in, there really isn't that much of a home theater performance difference between the 2011 and 2012 except for the added bonus of USB 3. (Lots of speculation that the next Mini this Fall will be a substantial, rather than incremental, step forward for the line.) The first crop of USB 3 products haven't been as reliable as Firewire or Thunderbolt. Perhaps the USB 3 controllers and hardware have improved since, but kragger's suggestion of the GoFlex line is a good one, hedge your bets. I use them, some I just pop the drives out of them when I find them on a good sale, some I use as external drives or backup drives, but if you do happen to experience any issues with USB 3 you can relatively inexpensively switch to a different adapter. It's a pretty smart system they've set up.
and, while it seems quite excessive and expensive, Thunderbolt.
I've mentioned it on previous threads but I've had good experiences booting 2011 Minis off of SSDs in Thunderbolt enclosures: a portable Seagate GoFlex adapter, a LaCie Little Big Disk and a LaCie 2Big. Thanks to TB you don't have to open your Mini to swap an SSD in, risking damage and protecting your warranty and/or Applecare coverage. If your 2011 Mini has the stock, small 5400rpm drive and
you plan to do a little serving and multitasking, you'll benefit from a faster boot drive. Those thunderbolt enclosures have all worked very well for me and many other Mac users--at the moment I have a 256GB SSD in the Seagate, two 4TB 7200rpm Seagate drives in the 2Big, and a 256GB SSD and a 1TB drive set up as JBOD in the Little Big Disk. The two LaCie I bought as refurbs from MacMall at a substantially reduced price, immediately voided their warranty repurposing their internal drives and swapping my own bigger faster drives inside, plus the LaCies each have a second TB port for daisy chaining. But even as refurbs they were a little more expensive than roughly comparable drives with FW 800...at the moment you can get that refurb 1TB LaCie LBD for $160 from MacMall, that's not bad for a dual drive enclosure with two Thunderbolt ports that you can put bigger/faster drives or SSDs inside with two decent 500GB Hitachi drives left over...but if you really are concerned with keeping your expenses low nothing
with Thunderbolt will ever meet your requirement. There is a potential risk with some USB 3 enclosures, a good number of users have reported shielding issues, BT and wireless interference, and volumes dropping off randomly...if you do decide to get something with USB 3 make sure Mac OS X users have recommended it, and that it is 1) either so reasonably priced you can easily replace it or 2) it's on a combo enclosure so you have the option to connect over firewire or the Seagate GoFlex. Even then, though, I've come across threads where a combo enclosure with USB 3 and firewire, the MiniStack from OWC, only connected over firewire can cause strange behavior, just from the mere presence of the un-used USB 3 port. Take home point, USB 3 on Macs isn't the fast inexpensive be-all end-all just yet.
Some other things to factor in...one drive won't cut it, you need backups that aren't connected to your system and aren't even on the network, so they're protected from an electrical surge. (I now have 5 different copies of my 800GB or so iTunes music library, I never want to have to create that again...) A big negative (for me) with those commercial Seagate GoFlex and WD MyBook type drives is that the only way you can get a warranty replacement for the drive is to send them the drive, still untouched in its cheap plastic enclosure. That means no removing the drive to attempt any data recovery before sending it in, no erasing your personal data before sending it in. That's another reason why you don't want just one big 4TB drive no matter how tempting the price...if there's a problem with that you're screwed, you'd lose your backup volume, your media, everything. That's also why many of us buy some empty enclosures and devices and put our own bare drives inside them--that way you can open and swap and move drives around to your heart's content--all the while protecting your warranty on both drives and device hardware.
So, even if you think all your media will fit on a single large drive for now, buy two.