I happen to live in Austin! Here's what I've found so far that I like. I've noticed that prices here are a little higher then other places.
New Bohemia - on South Congress. It's big, carries a nice selection of stuff for both guys and girls including vintage clothing, jewelry, shoes and some cool house stuff.
Goody Two Shoes - Not vintage, but on South Congress. They carry lots of shoes and purses in the front and hipster stuff in the back. I've gotten some beautiful vintage-inspired heels there for not a lot of money.
Uncommon Objects - Also on SoCo just up from New Bohemia. I love this store. It looks like an estate sale went mad! There are tons and tons of little spaces to run through and they do carry vintage clothing and furniture. The clothing is mostly on the left hand side when you walk in.
Amelia's - On South First street, arguably the most high end vintage place I've found here. Her collection is amazing, she knows her vintage and she's been dealing in Austin for 20+ years. I've found many a drool worthy item in her store. Her prices might not be as good as some places but if you need a rental or you really want to drop duckets on something nice she's a great place to go.
Flashback - Also on South First, north of Amelia's. I like this place too! They've "re-opened" recently, though I never knew they'd closed. It's an old house with tons of vintage clothing. I've found great deals there and some not so great deals. Velvet clutch in great condition for $10, awesome. Vintage house dress from the 50s with stains and tearing for $45, not so much.
On South Lamar the plaza with the Alamo Theater in it, has at least one vintage store, but it's been years since I've been in it.
There's Blue Velvet vintage on the drag and I think they have a second location on North Loop. The one on the drag is big, lots and lots of stuff, most of it seemed to be mid-60s through 80s though. There's also Cream vintage on the Drag and one more place that escapes my mind right now.
Oh, Buffalo Exchange is also up there. I've had mixed luck in this BE, they don't sort their vintage out on a separate rack, so be prepared to dig. Also, the staff is only so-so on helpful end. The girls I've talked to think that vintage means '70s and '80s. Still, I've picked up some nice stuff there with a little digging.
Room Service On the North Loop. Love this place too! Loads of vintage house stuff, bakelite, lamps and clothing. There was another vintage place on North Loop but they've moved, I'm not sure where. I think there's yet another vintage store across and west of Room Service but can't remember the name of that one either!
Also, there's Atomic City, over on 17th near the drag. Not vintage, but a great store lots of Kitsch and he carries Remix Vintage shoes and Lucky Lou shoes!
Austin is a big city and there's a ton of stuff here, I've probably forgotten about half of what I know exists, feel free to shoot me an email if you want more information on anything!