Every weapon or helm intended for a specific class has the chance to spawn with an inherent bonus to individual skills (inherent meaning they have nothing to do with the rare or magical mods). Paladins have it slightly different, as scepters (which are non-class-specific) get the skills bonus while shields (class-specific) can only get resists or %ed/+ar. Amazons also have it slightly different, as bows, spears, and javalin get bonuses to an entire skill tree (bow or spear/jav, not passive).
In the case of individual skills, a particular item can spawn at most 3 inherent bonuses, with a maximum of +3 to each. In the case of Amazon skill trees, you can only get a bonus to one tree and the maximum bonus is also +3.
I have definitely seen Sorceress Orbs with +1 or +2 to all skills as a rare mod and a couple inherent bonuses to individual skills. I have one right now that gives +2 Sorceress skills, +1 Energy Shield, +2 Chain Lightning, and +1 Meteor. You'll also remember the godly duped scepters back in classic with +2 Paladin skills, +3 Blessed Hammer, +3 Concentration, etc. It's even possible to find a rare claw with +2 Assasin skills, +3 Lightning Sentry, and +3 Death Sentry, although highly unlikely. But, I can't remember ever seeing a bow or javalin with inherent bonuses on top of rare or magical mods. Otherwise you would hear about godly (non-runeword) bows with +2 Amazon skills and +3 to bow skills, or godly javalin with +6 jav skills (+3 magical mod and +3 inherent).
So to answer your question, Amazon items can't, but every other item type can. I'm about 95% sure of this.
EDIT: Ok, so I just went and found a magical set of Matriarchal Javs with +1 jav/spear inherent, so that basically contradicts everything I just said. Maybe when you roll a +skills magical/rare mod it overrides the inherent bonus instead of adding to it, I dunno.
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