I've experienced some house-rules regarding what you're asking for. I'll try to summarize what I can remember as good as I can (it was a long time ago).
I'll start with the most obvious one: you can't buy them, they can only be given to you by the game master and you get nothing in exchange. This is, of course, quite interesting when it comes to background and character development, but as you've specifically asked for some kind of buying mechanism, I'll leave this method here just for completeness.
When we played Version 3, we decided that it would be cool to be able to buy flaws for our characters for developing them further and making their backgrounds richer. Our game master agreed but heavily limited the possibilities. We would not have the right to buy them directly, but would have to ask the GM for any flaw we wanted to have, give at least some reason for it, mostly things that had just happened ingame or that could be explained by our characters' background stories and he would then decide, what we'd get in exchange. This could be anything from some karma points to rare equipment (or not so rare things), spirits or what have you. The GM would decide, take it or leave it.
In another group, we could simply "buy" them and get their cost as karma points to advance our characters (while having to deal with the negative effects, of course), but had to ask the GM whether it was OK for our characters to buy them (so we couldn't just throw in a lot of them for some quick karma).
In most other cases, we would simply use the first method I described, where you can't "buy" any flaws, but can only get them from the GM.
Personally, I like a mixture of the first and the second method. In most cases, the GM would simply give your character a flaw if it fits the events he/she has recently been through. In some rare cases, however, you might decide that a certain flaw was just perfect for your character right now, but you just don't want to simply make life for your character harder, but get something in return - if your GM is OK with it (and it was agreed upon up front), you might ask for something in return, as you just deliberately gave your character a flaw.
All in all I'd say that the most important rule about rules can be applied to this question: they are mere guidelines that one should (if the other players and the GM agree, of course) bend or even abandon if that makes the game better for them.
If you want some advice, I'd say you should simply sit down with your GM and the other players (or your players if you're the GM) and talk about it, then give the method you can all agree on a try and see how it affects your game experience. If it improves it, keep it; if not, try something else or go back to default.
Edit: As Trajan pointed out, my answer was lacking the impact on the game and information about balancing, so here goes:
Impact on the game
As far as I recall, the impact on the game was not that huge, as not every player wanted to actually give their character additional flaws. I do, however, recall one thing. I was playing a quite vindictive character (I can't recall whether or not the character actually had the flaw, though) that started a feud with another player's character. That character ended up mutilating (lost an arm and was almost beaten to death) and humiliating my character. After quite an elaborate piece of planning and plotting, my character finally got his revenge and killed the other character. For that I decided to give my character the Bad Reputation flaw as I figured that an act like my character's revenge would not go unnoticed for long. I can't remember the rating of the flaw, sorry, but I remember losing some contacts and even get shunned by other players' characters from time to time. In return for giving my character this flaw, the GM would grant me some additional freedom in planning my character's revenge (which was quite awesome).
That wasn't the biggest impact, I guess, but it did lead to some interesting scenes with NPCs and even PCs (that would've also been possible without the actual flaw, I guess).
When we could "buy" flaws for some quick karma points, the impact was quite small, though. You can only buy so many flaws until you kind of put a gun to your character's head. The amount of karma you get from flaws is not that huge, but it may enable you to get that next attribute point NOW instead of after the next run.
Balancing
To be honest, I have no remembrance of any actual balancing rules being established. The GM would either decide on the spot or even weave decisions into the plot of the next run. For example, if a player wanted to give his character an additional flaw and accept the consequences (like losing contacts, having a harder time or whatever) and the GM knew that he always wanted to have a certain piece of hardware that he could never get for lack of money or contacts, he would then equip that player with that certain piece hardware (or, you know, the typical "prototype" of the corp that hired the Runners) and let him keep it after the run was completed (that actually leaves a lot of freedom for adjusting the balance later on - for example could the corp decide that they wanted their hardware back and the runner would suddenly face an addition enemy or something like that).
I'm sorry, but the balancing was never my concern, so the above part is mostly inferred from my experience.
When players simply "buy" flaws to get the free instant karma, everything balances itself out automatically, as the negative consequences would annoy or even hinder the character (of course the GM has to really enforce the flaws).
Final thoughts
Looking back, I guess the whole point of allowing players to buy flaws after character creation is to enable them to apply some additional touches to their characters, as well as to enable them to make the game a bit more challenging (this applies to characters that have been around for some time) and/or interesting.
All in all, I guess that this particular house-rule kind of balances itself as the players are in charge. If they think their characters have enough flaws, they won't add more. If they are given one by the GM, they might even that out with karma and so on).
Hope I was able to give you some hints on your question, maybe even answer it.
