Atom is certainly the oldest of the words and also comes first alphabetically, hence it is the logical place to start. It is first seen in the late 15th century and taken from the Latin atomus meaning 'indivisible particle'. Even though we are speaking about sub-atomic particles from hereon, this definition still fits as this is indeed the smallest state any of any element, and smaller and it is quite simply something else. Latin took the Greek atomos meaning 'uncut, unhewn, indivisible' from a 'not' and tomos 'a cutting'. What had been ancient speculation by Greeks such as Leucippus and Democritus, saw a revival in 1805 by the British scientist John Dalton.
Quark is, for a particle only named just fifty years ago, still questioned. As a sub-atomic particle it was certainly named by US physicist Murray Gell-Mann who, in correspondence with the Oxford English Dictionary, informed the editors he took it directly from James Joyce's Finnegans Wake but already had the sound in his head before he found the word in print. Now this is said to be plausible as Gell-Mann's parents emigrated to the US from Austria-Hungary and German quark does exist (its meaning of 'curds, rubbish' is hardly relevant here). The questions concern the pronunciation which in US circles is generally pronounced to rhyme with 'stark' and in the UK more often rhyming with 'walk'. Note George Zweig, who deserves equal credit in the work, suggested the name ace.
Ion, as a noun, came into being when suggested by polymath the Rev William Whewell to physicist and chemist Michael Faraday. Whewell understood the Greek ion, being the neuter present participle of ienai 'go' came from the Proto-Indo-European ei 'to go, to walk' and perfectly describes how electrons move towards the electrode of opposite charge. Incidentally, this ancient root can be traced to words with identical meaning in Greek, Latin, Old Irish, Irish, Gothic, Gaulish, Sanskrit, Avestan, Old Persian, Lithuanian, Old Church Slavonic, Bulgarian and Russian.
Electron was coined by Irish physicist George J. Stoney in 1891. He combined 'electric' with 'on', as seen in 'ion' (below) as the flow of electrons is, in a most basic sense, what the layman refers to as 'electricity'.
Proton was coined in 1920 by the English physicist John Rutherford. He used proton as the neuter of the Greek noun protos meaning 'first'.
Neutron is 'the electrically neuter part of the atom' and named in 1921 by US chemist William D Harkins, he taking 'neutral' and 'on' (see 'ion') to produce a word which has a basis in 'neuter' and originally referring solely to gender in the sense 'not capable of breeding'.
Neutrinos are particles smaller than a neutron, the term coined by Italian physicist Enrico Fermi and ultimately shares its etymology with 'neutron' (above).
Photons are units of electromagnetic radiation (light to you and I), and derives its name from the Greek photo 'light' and the suffix 'on' (see 'ion'). Note the Greek photo can be traced back to Proto-Indo-European bha 'to shine'.
Baryon comes from the Greek barys 'heavy' and the addition of 'on' (see 'ion').
Fermion is a name coined by Paul Dirac and inspired by Italian physicist Enrico Fermi with the addition of 'on' (see 'ion').
Lepton is named from the Greek leptos 'small.slight' and derived from lepein 'to peel' and ultimately from Proto-Indo-European lep 'peel, shave, to scale (from fish)'. Here the suggestion is the lepton is a weak force and shares a root with 'leper'.
Mesons are intermediate in mass between protons and electrons hence, with the suffix 'on' (see 'ion') the Greek mesos or 'middle' was used.
Hadron uses the suffix 'on' (see 'ion') to follow the Greek hadros 'thick, bulky' as well as 'great, large, ripe'. This prefix comes from the Proto-Indo-European root sa 'to satisfy' and shares an origin with 'sad'. Scientist working at the Hadron Collider (a fabulous potential pub name) might have their own opinions as to their work being related to 'thick' and 'sad'.
Higgs boson is the Holy Grail for physicists - the Holy Grail that is until they discover something ever deeper - and is named after Peter Ware Higgs CH FRS FRSE and Satyendra Nath Bose FRS. Neither men gave the alternative name of the 'God particle' to the Higgs boson, this most often attributed to Leon Lederman as the author of the book The God Particle: If the Universe Is the Answer, What Is the Question? (catchy isn't it?) but actually came from the publisher (yes, been there!) after Lederman originally came up with the phrase the "Goddamn particle".
Pions were named from the Greek letter pi, itself from the Hebrew where it meant 'little mouth', together with the suffix 'on' (see 'ion').
Positron was coined in 1933 and simply takes the first part of 'positive' and the ending of 'electron' to describe itself.
Muons were once known as the 'mu meson' but scientists agreed upon the shorter version. Hence the 'meson' (see above) took on the Greek letter mu, itself derived from the Egyptian hieroglyph for 'water' and which also formed the basis for the Polish word for 'slime', the Sanskrit word for 'urine', and the Avestan word for 'excrement'.
This is why language is so wonderful. In the modern world of science we need to travel back thousands of years, only to discover the 'water', 'urine' and 'excrement' all, etymologically speaking, stem from the same thing.