> Presumably someone figured out a way to prevent timing attacks against your own account - what is it?
As long as the salt has sufficient entropy, this isn't a problem. So instead of generating the salt from the username / etc, you use a random salt and store it.
> How does it work?
Effectively, by leaking internal state of the cypher / hash through timing variations. The most common ways of doing so are either through data-dependent table lookups or through operations that may be microcoded or otherwise take variable time (multiplications, rotations sometimes, divisions, modulo, squaring).
See, for instance, http://cr.yp.to/streamciphers/leaks.html - although note that this is dealing with stream cyphers not hash functions. In particular, the linked paper describes an effective timing attack against AES by taking advantage of processor cache effects on a data-dependent table lookup. I'd give it a read - it's quite interesting.
SHA256 is pretty good w.r.t. being close to constant time for a fixed input length. Not perfect, but meh. It uses bitwise xor and and, rotates, shifts, and addition, none of which are generally variable-time (although note that on some platforms rotates are variable-time).
For most things, SHA2, by which I mean the newer variants, works reasonably well. In particular, you store SHA2(password xor random_salt xor pepper) and discard the original password. Store the salt in the database with the user, and if you want to get really fancy you embed a single random value ("pepper") in the application code - this is a kind of last-ditch effort to hopefully prevent user passwords from being leaked even if the database is leaked.
If you really want to get fancy, you also embed a couple "canary" accounts (random made-up accounts) in your database, with a passive device on the network that screams bloody murder if any of those accounts ever get successfully logged in to.
However, that being said, that doesn't really answer your question.
A couple things:
1) You don't want to use SHA, generally. You want to use a proper KDF (key derivation function). Why? Standard hash functions are designed to be fast and not take much memory. Which means it is a whole lot easier to crack.
2) If any of the user authentication is in a language that you cannot disable optimizations in, and you cannot look at the assembly code coming out, you cannot prevent timing attacks. You may be able to mitigate them, but that is all.
3) In general, if a KDF / hash function doesn't use any data-dependent table lookups / pointer chasing / control flow, and doesn't do any complex functions (multiplication, etc), it's probably relatively safe from timing attacks. Otherwise... Not so much.
4) Theoretically, you need cooperation of the kernel, etc, to truly be safe from timing attacks. Among other things, context switches could leak information. In actuality... It's definitely possible but I don't know of anyone who has made it work.