With the release of the 3rd edition D&D system, the rules covering a character's skills have been greatly updated. Below is a mapping of the Spelljammer proficiencies from 2nd edition mapped to their new counter-parts.

Proficiencies to Skills & Feats Map

Ambidexterity(CSH) Two-Weapons Fighting feat (or Ambidexterity feat in 3e)[PHB]
Astronomy(WCC) Knowledge (wildspace) skill[PHB]
Balance(WCC) Freefall feat
Boarding Pike(SJR1) Martial Weapon Proficiency feat[PHB]
Carpentry (Spelljamming)(WCC) Craft (carpentry) skill[PHB]
Cartography(CSH) Craft (cartography) skill[PHB]
Fast-Talking(CSH) Bluff skill[PHB]
Fire Control(WCC) Wildspace Survival skill[PHB]
Fortune Telling(CSH) Bluff skill[PHB], Knowledge (arcana or religion) skill[PHB], and/or Perform (act) skills[PHB]
Freefall(WCC) Freefall feat
Grappling Hook(SJR1) Exotic Weapon Proficiency feat[PHB]
Heraldry (Space)(CSH) Knowledge (nobility and royalty) skill[PHB] or Knowledge (local) skill[PHB]
Languages, Space(WCC) Speak Language skill[PHB]
Large Weapons (Ship-Mounted)(CSH) Profession (siege engineer)[DMG]
Leadership(WCC) Despite the name, this isn't analogous to the Leadership feat from the Dungeon Master's Guide. Leave this one to prestige classes, like the Stellar Corsair's "Inspire the Crew" ability.
Looting(CSH) Search skill[PHB]
Navigation, Celestial(WCC) Profession (wildspace navigator) skill[PHB]
Navigation (Phlogiston)(CSH) Phlogiston Sense feat
Navigation (Wildspace)(CSH) Profession (wildspace navigator) skill[PHB]
Observation(CSH) Listen skill[PHB], Spot skill[PHB], Alertness feat[PHB]
Planetology(CSH) Knowledge (planetology) skill[PHB]
Planetology(WCC) see Spelljamming History proficiency
Sail Manipulation(WCC) Profession (spacehand) skill[PHB]
Semaphore(WCC) Speak Language skill[PHB]
Shipwright(CSH) Craft (shipwright, spelljammer) skill[PHB]
Signaling(CSH) Speak Language skill[PHB]
Slow Breathing(WCC) Wildspace Survival skill
Slow Respiration(CSH) Slow Respiration feat
Spacefighting(SJR1) Freefall feat
Spacemanship(CSH) Profession (spacehand) skill[PHB]
Spelljamming(CSH) This proficiency will be modeled by the ship to ship combat system.
Spelljamming History(WCC) Knowledge (history) skill[PHB] or Knowledge (local) skill[PHB]; needs to specialize to particular world or time period
Survival (Wildspace)(WCC) Wildspace Survival skill
Weapon Loader(WCC) Profession (siege engineer)[DMG]
Wheel Lock Pistol(SJR1) Exotic Weapon Proficiency (firearms) feat[PHB]
Zero-Gravity Combat(CSH) Freefall feat

Footnotes

(CSH)Complete Spacefarer's Handbook
(SJR1)Lost Ships
(WCC)War Captain's Companion Boxed Set, Book 1
[DMG]D&D Dungeon Master's Guide
[PHB]D&D Player's Handbook