The shoes were the Red Hidden-Heel High Top Wedges by River Island, however Joe Boxer of K-Mart made an identical pair. Last I heard they were on clearance, so they won't be around to much longer. It used to be a lot more valuable, but ever since the Joe Boxer became known, not as many people are after the SA pair.
Worn in: Asylum of the Daleks
All Saints Black Jules Shearling Black Biker Boots
The shearling version is very hard to find, but there is a shinier version that is pretty common. They were on clearance on All Saints site recently. Here's a tip: my pair came missing one of the straps, so I contacted All Saints on Facebook and they sent me two new straps free!
Worn in: The Bells of St. John (outfit #1), The Bells of St. John (outfit #2), The Rings of Akhaten
Red or Dead Silver Shirley Glitter High-Heels
These can be found of eBay reasonably often.
Worn in: Cold War
F-Troupe Black Nubuck Wedges
I've also seen these described as "slot-eye" wedges. They are rare, but it is possible to find the alt version and color alts. Some people have even successfully dyed the alternative color wedges with suede dye.
Worn in: Hide, Nightmare in Silver
All Saints Taupe Jules Biker Boots
These boots are the color twins of the black shearling version she wears in The Bells of St. John and The Rings of Akhaten. They were on clearance on the All Saints site recently, and they do make eBay appearances.
Worn in: Journey to the Center of the TARDIS (outfit #1), (and probably) Journey to the Center of the TARDIS (outfit #2)
F-Troupe Burgundy Knot Wedges
They seem to come and go in rarity. The good thing about F-Troupe is that they make many versions of the same shoe, so you can sometimes find this in a different color leather, or the same shoe but made as a flat.
Worn in: The Name of the Doctor, Doctor Who Proms Minisode
Dune Genius Leather Wedge T-Bar
These were shown for a brief moment in the Doctor Who Bonus Minisode. I think they're kind of summery and cool.
Worn in: Doctor Who Bonus Minisode
Topshop Chelsea Alexy Boots
They are pretty easy to find; eBay regular appearances. But they usually still sell for higher than I think they should.
Worn in: The Day of the Doctor
Topshop Metal Trim Boots
They are not too rare, but still a bit expensive. Uhh, can we stop with the nearly-identical ankle boots? Though I like these better than the Chelsea Alexy boots. Also, apparently on some sites these were labeled as "all mine" boots, and on others as "amelia lily".
Worn in: The Time of the Doctor (outfit #1)
Dune Astor Black Lace Up Wingtip Block-Heel Shoes
These were originally mis-identified, and this was only realized with the better photos from season 8 filming.
Worn in: The Time of the Doctor (outfit #2), Season 8
River Island Brogue Ankle Boots
Worn in: Into the Dalek (outfit #1)
KG Selina Shoe Boots in Rust by Kurt Geiger
These may still be found on clearance on some sites. My pair is very comfortable, but slightly too big, though they are my usual size.
Worn in: Season 8 Robots of Sherwood
Kurt Geiger GOSSIP High Heel Platform Shoes in Black
Notice how she swings them by the straps in the ep?
Worn in: Listen
Ash Cool Wedge Sneakers in Black
This style is pretty popular right now, so it shouldn't bee too hard to find alts if this is out of your price range. Original link here: http://www.shopbop.com/cool-wedge-sneaker-ash/vp/v=1/1537482616.htm?folderID=2534374302024643&colorId=20742&extid=affprg_CJ_SB_US-3642631-ShopStyle+CA-5676018