I've been looking up allophony for these. Many of these have allophony like [m] ~ [b] or [l] ~ [r] which means it'll be a bit misleading to assert that the language "lacks /m/" or "lacks /r/".
Notation: [A~B] means that [A] and [B] are in free variation. [A B] means that [A] and [B] are positional allophones. Same goes for cases of [A] … [B] in the distance. If two of these occur next to each other, I've marked [A B|C] … [D], where one phoneme is /A ~ B/, the other is /C ~ D/.
Code:
::POLYNESIAN::
Hawai'ian p m n k ʔ v h l 8
Tahitian p m t n ʔ f v h r 9
Māori p m t n k ŋ f w h r 10
Niuean p m[t] n k ŋ f v [s] h l 10
Samoan p m k ŋ ʔ f v s h l 10
Rarotongan p m t n k ŋ ʔ f v s h r 12
Tongan p m t n k ŋ ʔ f v s h l 12
::OTHER OCEANIC::
Roro p b m t n k ʔ h r 9
Mekeo p m t n k ŋ ʔ f s l 10
Lote p m t n k ŋ s x h l r 11
MussauEmira p m t n k ɣ ŋ β s l r 11
Wuvulu p b m t n ʔ f w h l r j 12
::IROQUIOAN::
Onondaga [t d]n ʤ [k g] ʔ w s h j 9
Cayuga [t d]n ʦ k kʷ ʔ w s h r j 11
Cherokee m t n ʦ k ʔ ɰ s h l j 11
Mohawk [t d]n ʤ [k g] kʷ ʔ w s h[l r] j 11
Oneida t n ʦ k kʷ ʔ w s h l j 11
Seneca [t d]n ʣ ʤ [k g] ʔ w s ʃ h j 11
Tuscarora t n ʧ k ʔ w θ s h r j 11
::CADDOAN::
Pawnee p t ʦ k ʔ w s h r 9
Wichita t [n]ʦ k kʷ ʔ w s h [ɾ] j 10
::ALGONQUIAN::
Cheyenne p m[t] n[ʦ] k ʔ v s[ʃ x]h 10
Menominee p m t n ʧ k ʔ w [s ʃ] h j 11
Arapaho [p b] t n ʧ k ʔ w θ s x h j 12
::NASAL-ALLOPHONY AMAZONIAN::
Pirahã p[b m]t [n] k[g] ʔ s h 8
Cubeo p[b m]t[d n] ʧ k w x r j 10
Xavante p[b m]t[d n|ʦ~ʧ|ʣ~ʤ ɲ] ʔ w [s] h r [j] 10
Barasana p[b m]t[d n] [ʧ] [ʤ] k[g ŋ] w [s] h r [j] 10-11
Tuyuca p[b m]t[d n] [ʤ ɲ]k[g ŋ] w s h r [j] 11
Karajá [b m]ɗ[d n] ʧ ʤ k w θ ʃ h l ɾ 12
::OTHER AMAZONIAN::
Puinave p m t n k (w) s h (j) 7-9
Barí b m t d k s h ɾ r j 10
Iquito p m t n k w s h r j 10
Tiriyó p m t n k β [s~ʃ] h [ɾ~ɽ] j 10
Arabela p m t n k w s ʃ h r j 11
Jamamadí b m t n [ɟ] k (ʔ)ɸ w s h̃[l~r] [j] 11-12
Huaorani p b m t[d]n [ɟ]ɲ k g ŋ w [ɾ] [j] 12
Ikpeng p m t n ʧ k g ŋ w l r j 12
::PAPUAN MISC::
Iau [b m]t[d n] k f s 6
Rotokas p b t d k g 6
I'saka [p|b m]t[d n] k [ɸ]w s j 8
Nasioi p b m t d n k ʔ 8
Taoripi p m t k f s h l 8
Abau p m[t d]n k w s h[l r] j 9
AitaRotokas p b m t d n k g ŋ 9
Gadsup p m t d n k ʔ β j 9
Namia p m t n k w l ɾ j 9
Ekari p b m t d n k w gʟ j 10
Sentani p m t n k f w h l j 10
Koiari b m t d n k g f ð h r 11
Kwomtari p b m t[ɖ]n k g [ɸ β] s [ɭ]r 11
Tigak p b m t n k g ŋ s l r 11
Awa p b m t n k g ʔ w s r j 12
Ese p m t n ʧ ʤ k ʔ β s h r 12
Fas p m t n k ʔ f w s r j 12
Tifal [p b]m t[d]n [k ɣ]ŋ f w s l[ɾ] j 12
Yimas p m t n [c] ɲ k ŋ w [s] ʎ r j 12
::OTHER::
Miyako [p b]m[t d|n] [k g|ŋ] f v [s ɕ|x] ɾ 9
Keuw p b t d k g w s l j 10
Maxakali p[b m]t[d n] k[g ŋ] ʔ ʃ h j 10
Palauan [p b]m t d[n] [k g]ŋ ʔ [w|θ ð]s l r [j] 10
Ainu p m t ʦ k w s h r j 11
Irantxe p m t n k ʔ w [s ʃ] h[l~r] j 11
Maranao p m t k ŋ ʔ w l r j 11
Warao p m t n k kʷ w s h r j 11
Bandjalang p m t c ɲ k ŋ w l r j 12
Comanche p m t ʦ k kʷ ʔ w s h j 12
Ket [p b]m t d n [k g]ŋ [q ɢ] s[ç] h ɮ [ʝ] 12
Meänkieli p m t n k ŋ ʋ s h l r j 12
(Added Iquito and Meänkieli; left out Karitiâna since WP also report /j/ and /ʔ/.)
Nasal/voiced stop phonemes seem to be quite common; Pawnee and Rotokas are the only examples to truly lack nasality in here. Possibly Keuw, but I can't seem to find what this one even is. Phonation variation is less common, mainly found in Iroquioan; for stops also Miyako, Tifal, Ket and Palauan; Kwomtari has /p/ ≠ /b/ etc. but [ɸ] = [β].
There are several examples of [ɟ] ~ [j] allophony in the Amazonas (Xavante, Tuyuca, Jamamadí, Huaorani, Barasana) and a couple of these also have [tʃ] ~ [s] (Xavante, Barasana). Any other [±continuant] allophony is very rare though. There's one example each of [p] ~ [ɸ] (I'saka), [d] ~ [ɾ] (Tifal), [ɖ] ~ [ɭ] (Kwomtari), [t] ~ [s] (Niuean) [c] ~ [s] (Yimas) and [k] ~ [ɣ] (Tifal again). Also I don't know how Ket works exactly but the
surface inventory includes [β ɣ ʁ] coming from somewhere so I'm assuming that's an example of more widespread spirantization.
Other observations: consonants in the palatal/postalveolar stop/affricate/nasal region seem to be almost entirely limited to Iroquioan and Amazonian languages. Menominee and Arapaho have /tʃ/; Yimas and Bandjalang have /c ɲ/; Ese has /tʃ dʒ/.
—It's also interesting how voiced/voiceless contrasts are fairly common but plain/aspirated contrasts are not found at all, especially when /h/ is really common regardless.
I'm tempted to attempt some sort of a cluster analysis next (inventories placed at a distance from each other by the number of differences; something like /m/ versus /m~b/ or /r/ versus /ɾ/ might count for less) but I'd have to look for suitable software first.