So, I was surfing Cracked.com when I came across this interesting little article.
Electrosensitivity would be absurdly crippling in Shadowrun, but it doesn't actually exist so we can ignore it.
Sunlight is a commonly used allergy so new discussion on it is unnecessary.
The other four allergies, however, have the potential to ruin the days of some characters. A really sadistic GM could pre-build characters with one of these allergies. A more thoughtful GM could give these allergies to NPCs both friendly and hostile to provide extraction runs with a little spice or give the PCs more tactics against a powerful foe.
First, have exercise or, specifically, physical exertion. Exercise induced anaphylaxis makes the Infirm Quality seem downright merciful, particularly taken at Severe. Any Athletics test, gymnastics melee combat, or even running, would activate the allergy. Characters with this allergy should just be thankful that it is impossible to make a weapon out of exercise. On the other hand, it doesn't present too much trouble to vehicle riggers and couch-potato characters in general.
Then we have the allergy to Cold. Honestly, like allergy to sunlight or any other environmental allergy your mileage varies depending on environment. In the tropics, cold is a hell of a lot easier to avoid than sunlight. In the far North, sunlight is easier to avoid than cold. Any time that cold resistance would be useful, such as being trapped on a tundra by angry Eskimos or trapped in a meat locker by Mafiosos, characters with this allergy are screwed. Weapons to avoid include fire extinguishers, capsule rounds filled with liquid nitrogen, icicle knives, and elemental cold spells. Free points if you're cyberpirating in the Caribbean with Black Jack Savage.
Semen - okay, this really only comes up for pornomancer characters. And most people with semen allergies are only allergic to specific people's semen. Having a character with an allergy to Damien Knight's semen is almost free points unless the GM wants to pull out Firewatch teams with squirt guns full of the stuff. However, it is apparently possible to be alergic to one's own semen, which must totally suck for vampires with that allergy. They can have their prostates removed but doing so would instantly reactivate their regeneration causing their prostates to grow back. This is one of the reasons I prefer the SR3 regeneration rules. If one's GM allows this allergy expect sexual encounters with a certain corporate bigwig to become major plot points.
And most dangerous of all - Water. The water allergy happens to be the single most debilitating allergy anyone could have, even beyond the exercise allergy, particularly at severe. Living on a planet covered with the stuff ain't gonna be fun at all.