When do you apply the social penalties for odd or excessive obvious cyberware?

The rules suggest all times except when Intimidating another, which makes sense because looking like a Grade-A Freak should help you then.

But what about Negotiation? Reasonably Negotiation is as much a battle of wits as anything else, even if he doesn't like your looks it's not going to help Mr. Johnson somehow out negotiate you. If anything something like an Obvious Cyberskull should help you because instead of thinking about his next counter-point Mr. Johnson will instead be thinking about your Cyberskull, wondering if it hurts and how you could possibly have that thing in your head.

Etiquette I can see, it's a matter of convincing your Contact to go to the trouble of finding what you want.

Leadership? For most things a Shadowrunner would want to convince somebody to do looking like death incarnate would be a help, and it never hurts to have your cannon fodder more afraid of you than the enemy.

Instruction would be a real pain because you want your student to concentrate on your words, not your looks.

But overall I personally never use any social penalties because I don't want to give them to my players when their contacts have cyberware. . .

Player: Right, I've got good reputation 2 and my contact is a Cyberzombie with minus 2 points of essence. . . so my TN is 4 and his is 13 right?

The penalties are all based on GM fiat. Personally, I don't apply modifiers from this stuff when dealing with a Johnson (they're expecting runners to be chromed to the max) or many shadow contacts.

Where it really starts to come into play is with the "right" side of the law. Fast talking that Lone Star cop into thinking you're a janitor emptying the trash is a lot harder if you have an obvious cyberskull.

These modifiers are generally meant to represent a slightly alien mindset for those who with cyberware. Sure, your looks might not affect your ability to instruct someone in basket weaving, but your detacment from normal human thought might well do so.

I'd evaluate it on a case-by-case basis.

1. How does the audience react?
a) Suburban housewives would react differently than gang-bangers.

If the audience thinks its cool, then apply a bonus.

If you're trying to scare the audience (Intimidation), apply a bonus.

If you're trying to convince an audience and you scare them, apply a penalty.

And so on.

-Siege

As it is basically a roleplaying thing, it would be greatly advisable to eschew mechanics in favor of leaving it up to the GM and his or her portrayal of both the world and the people who live in it. Is worth noting, however, that cyberware penalties should not be so extreme. Yes, the really unsubtle stuff could be unpleasant in certain circles, but b and large, a certain degree of augmentation is acceptable throughout society.

Depends on the augmentation -- cyberlimbs going at 100k are going to be few and far between while datajacks are innocuous enough not to raise eyebrows.

Obvious cyberskulls, kid stealth legs and balance tails are outlandish enough to occasion comment almost universally.

-Siege

It should depend on the social situation.
In a corp high-society environment, most obvious cyber/bio/nano mods would be frowned upon. Anything bigger than a golden datajack/chipjack or the occasional discreet, brand-name cybereyes would not fit the strict dress code.

On the club scene, on the other hand, the all-chrone "robo" look is sooooooo 2050's... It's bio sculpting that's fashionable and nanotattoos are ubercool. Atleast this is how I see it. Strange skin colors, cat eyes, even fur.

In the barrens, big-time chrome should keep some of the gangers away - they usually won't want to deal with a real samurai. But the organleggers would see you as a walking cashbox...

And it changes geographically. In Seattle it might be as described abouve, but go to the areas affected by the Eurowars or their side-effects - Russia, Poland, Israel - and you'll find alot more cyber in replacement of limbs or eyes lost during the war. Add to this the complusary military service in Russia and Israel - especially the "reserve" duty. Now the government got you on its beck and call for life (45 days a year in the 2064 Israel between the end of the "standard" tour of duty and the age of 50), so adding cyber won't be a problem. So if you walk in the market at downtown Haifa, expect to see alot of cyber around you.