What Skill would you use for some one to try and appraise the value of something... such as gems or art, or even other goods?

Would you use a skill? Or just a straight Ability check Like Int or Cunning?

Perhaps Streetwise? Education? Or Lore? Lore doesn't really seem to fit of those three?

Negotiation is the go to for bartering and stuff like that. It goes into it in the Gear chapter and the Negotiation entry in the Skill chapter. AFB, but some circumstances, like black market deals and restricted items, can use either Streetwise or Knowledge (Underworld) (I don't remember which).

Negotiation Seems More of a Social interaction skill than a appraisal/Knowledge skill

Having a Good "Presence" just seems an odd Choice to say you have an Idea of what something might be worth.... Knowing how to talk your way through a trade/sale sure.

Applicable Knowledge skill.

Not saying it makes too much sense, but just that it's there. Negotiation itself applies to buying/selling/haggling, mostly, but the rarity modifiers are a good place to start. You can maybe check it out and apply it to a skill you think appropriate. Education I would say is default, but not enough to override another skill (no omnidisciplinary scientists allowed).

It seems to me that the actual appraisal itself would come from the appropriate Knowledge skill, but I can see an argument where Skulduggery might be a suitable alternative in some cases.

Once the appraisal is determined, negotiating the actual deal would be governed by the Negotiation skill, although I can also see Streetwise potentially being applicable.

Knowledge (Lore) for very old stuff, Knowledge (Xenology) for alien artefacts and the like, Knowledge (Underworld) for illegal items and contraband, and Knowledge (Education) for everything else.

Whatever skill seems most appropriate.

Negotiation for mundane items. "I bet I can talk someone into buying this for X"

Streetwise for illegal items. "Street value on this is around X"

Lore for specifically rare items "Wow... there's like only three of these and the last one sold for X at auction"

Education for niche or specialty items "There's a university on Dinglehouser that's buying these for it's anomalous materials lab"

so on...

You can also allow multiple skills options if it makes sens for the item in question:

"This is a very specific piece of medical hardware, appraisal is an Average Medicine, Hard Education, or Absurd Negotiation check. Your choice."

Don't forget Knowledge (Warfare) for military goods.