Hayes-McCoy in his HISTORY OF IRISH FLAGS mentions several Jacobite colours:

FOOT GUARDS "the Royal colours of England, St. George's cross and the arms of the four kingdoms," presumably a red cross, edged in white (?), with the arms of England, Scotland, France and Ireland as in the Royal standard in each quarter.

ANTRIMS "a red cross in a green field, in each quarter a hand proper coming out of the clouds, holding a cross of Jerusalem (i.e. one crossed toward the end of each limb, the lower one coming to a point) gold; at the centrc of the colour an Irish harp with a crown imperial with this motto 'In hoc signo vinces'.

BELLEW'S "bendy black and tawny or filarnot on the top, next to the spear, a crown imperial, and round it this motto 'Tout d'en haut'. In the centre the Irish harp and crown imperial. The colonel's colour has a small crown patee for distinction."

O'NEILL'S "white, in the centre a bloody hand, round it this motto 'Pro Rege et Patria"'. The colonel's colour had a similar distinction to Bellew's.

LOUTH'S "filarnot... with at their centre a crown imperial", and the motto 'Festina lente'. The company colours also had a blue cross.

LORD GRAND PRIOR'S (ex-Ramsay's) - colonel's colour white with a representation of a burning city, with the motto 'The fruits of rebellion' (which also appeared on the grenadier caps).

He takes these descriptions from "Thc Journal of John Sieplicus", a junior oficer in the Lord Grand Prior's Regiment, and the descriptions date from a Jacobite muster at Dundalk, 19th June 1690. The diary itself was published in 1912, edited by R.H. Murray.

A colour captured at the fight at Windmill Hill at the siege of Derry, and thus belongs to either Eustace's or Butler's, was yellow with the device of a phoenix rising from the flames and the motto 'Dum spiro spero'.

Two colours captured at Aughrim bore the motto 'Un Dieu, Un Roi' and 'In hoc signo vinces' respectively.

I'm afraid I do not have any information on the uniforms though, nor on the Hugenot regiments (but oh, what I'd give for some!)