Here are a few from "The Languages of New Guinea" by William Foley:
• Proto-Lakes Plain is reconstructed as having a consonant inventory of /p t k b d/.
• Iau has eight tones, but verbs are not lexically marked for tone; instead, they change tones to mark aspect/mood. There are also six aspect-mood particles, but those also change tones. Examples from the paper:
doe 'see' doe3 'look at, watch' (durative), doe8 'have seen' (resultative)
tai 'contact' tai2 'be falling' (telic, durative), tai4 'still being pulled toward' (incomplete), tai5 'has fallen' (telic, punctual), tai6 'alight at/on' (punctual, resultative)
y (declarative speech marker) y3 (simple response providing information), y4 (implied directive), y9 (strongly contrastive)
• Many languages in New Guinea have highly reduced pronoun systems. Kuman has four, with a number distinction only in the first person: na '1SG', no '1PL', ene '2', ye '3'. However, the verbal affixes distinguish three numbers (singular, dual, and plural) in all three persons. Some have no number contrast at all: Manem ga '1', sa '2', aŋk '3', and Golin lacks a third-person pronoun: na '1', i '2'. Some conflate 2SG and 1PL: Suki ne '1SG', e '2SG/1PL', de '2PL', u '3SG', i '3PL'. Nimboran apparently distinguishes between inclusive and exclusive first-person pronouns but doesn't have a number contrast in pronouns, but no examples are given.
• I'm quoting this next one because I don't get it at all:
• Kiwai has verbal prefixes that mark for whether or not the subject is first-person and suffixes that mark the subject's number (singular, dual, trial, and plural). The number of the object is marked by vowel alternations in the root for nonsingular objects, but there are also optional suffixes marking the same four numbers as are marked for the subject.Dani (Bromley 1981) exhibits a fascinating cline in this area. There are six independent pronouns, distinguishing three persons and two numbers. But the subject suffixes in hortative imperative mood neutralize the number contrast in third person. The hypothetical mood further conflates second singular with the third person form, leaving the second plural as the only distinct second person form. Finally, the future potential loses all person distinctions, with only a binary contrast for number remaining.
• Yimas has, in addition to singular, dual, and plural pronominal affixes, a paucal suffix -ŋkt, which can combine with plural pronominal affixes for subject and object.
And some others that I've picked up from various other places:
• Kensiu puts Germanic languages to shame: it distinguishes six levels of height (seven if the diphthong /ie/ is included), and also has a retroflexed vowel /ɚ/.
• Reduplicative infixation in Aslian languages.
• Kusunda has vowel harmony between /i ə u/ and /e a o/, but the two sets are in free variation in many words. Words with uvulars always have the lower set. Some high-frequency verbs mark the irrealis by shifting the vowels from the upper to the lower set, backing apicals to laminals (consonants in Kusunda are only distinguished by their active articulators; the passive articulator appears to vary almost freely) and velars to uvulars.
• Seri derived its definite articles from nominalized verbs of motion and location.