村雨葉織 / Murasame Haori: From the traditional garment haori??
豆籾平太 /Mamemomi Heita: ?? For the initials ??

ウイリアム・エテンシー / William Petenshy: William comes from William Shakespeare. His surname comes from petenshi (ペテン師), “swindler”.
デカーゴ・ミターマン / Decargo Mieterman: Decargo is a portmanteau of dekai, “big” (でかい) and ago, “chin” (顎). “Mieter” most likely comes from “meter” (in this case, either the gas meter, or the meter in poetry).
アルタモン夫人 / Mrs. Altamont: Altamont is a character in the chronologically final Sherlock Holmes short story, His Last Bow.
ダンカン・ロス / Duncan Ross: Duncan Ross is a character in the Sherlock Holmes story The Red-Headed League.
セルデン / Selden: Selden is a character from the Sherlock Holmes novel The Hound of the Baskervilles.

エライダ・メニンゲン: / Elyder Meningen: erai dame ningen (えらいダメ人間) means “incredibly bad person”. Also likely a reference to Princess Clotilde Lothman von Saxe-Meiningen, a character from A Scandal in Bohemia (see kb0312's post)
ベンヤミン・ドビンボー / Benjamin Dobinbough: Benjamin might be taken from Benjamin Franklin? Do binbō (ド貧乏) means “incredibly poor”.
トビー / Toby: From the dog Sherlock Holmes uses in his investigations in the Sherlock Holmes novel The Sign of Four/
ゴッツ / Gotts: Short for Gottsreich. Wilhelm Gottsreich Sigismond von Ormstein is a character from the Sherlock Holmes short story A Scandal in Bohemia.
コネット・ローザイク / Conette Rozaic: Conetto comes from the verb koneru (捏ねる), “to knead”. Rozaic comes from the word rōzaiku (蝋細工), which means “waxworks”.
ジョン・クレイ / John Clay: John Clay is a character from the Sherlock Holmes story The Red-Headed League.
ルンバ・マルマッチ / Lumba Marmacci: The name Lumba/runba (ルンバ）is an rearranged barūn (バルーン), or “balloon”. The maru in marumacchi might come from maru (丸), “round”.
コートニー・シス (旧姓: サイモン) / Courtney Sithe (née Simon): Sithe comes from the verb shisu (死す), “to die”.
イーノック・ドレッバー / Enoch Drebber: Enoch Drebber is a character from the first Sherlock Holmes novel A Study in Scarlet.
プロフェッサー / Professor: Most likely a reference to Professor James Moriarty, “the Napoleon of Crime” from the Sherlock Holmes stories.
クリムト・バンジークス / Klimt van Zieks:　From artist Gustav Klimt???
亜双義玄真 / Asōgi Genshin: ?? Shares the character “truth” (真) with his son. The character gen (玄) can mean “dark”, or “unclear”, so perhaps his name points to the “unclear truth”, as opposed to Kazuma’s “one truth”.

慈獄政士郎 / Jigoku Seishirō: Jigoku, when written as 地獄, means “hell”.
エブリデイ・ミテルモン / Everyday Mittlemont: Probably from the English “everyday” and miteiru mono (見ている者), “person who watches”, as a reference to his former occupation.
アンナ・ミテルモン / Anna Mittlemont: Surname taken from her husband.
ハリー・バリケード / Harry Barricade: Prison director, so a barricade?
ヒュー・ブーン / Hugh Boone: Hugh Boone is a character from the Sherlock Holmes short story The Man With The Twisted Lip.
ゴシップ / Gossip: From his occupation.
ビーナス / Venus: From the Roman goddess of beauty.
サンドイッチ / Sandwich: From his occupation as a sandwich man.
モーリス・デ・キルコ / Maurice de Quilco: de Quilco comes from dekiru ko (出来る子), “capable child”.
マルコ・ド・ジッコ / Marco d’Gicho: d’Gicho: d’Gicho comes from “dojikko[/i] (ドジッ子), “clumsy girl”.
マリア・グーロイネ / Maria Goullyone: Goullyone comes from guroi ne (グロいね), “grotesque, isn’t it?”.
マブドフ・ストロガノフ / Mabtov Stroganov: The surname comes from his brother. Mabtov comes from the tofu dish mabōtōfu.

ホテル・バンドール / Hotel Bandoor: The Hotel Bandō (formerly known as Bandō Hotel) is a location in the main series.(see kb0312's post)
アシタール寄宿学校 / Ashtar Boarding School:　Ashitar was the name of a meteorite that featured in Takumi's game Ghost Trick (known as Temsik in the localized version) (see kb0312's post)

袖ノ下正 / Sodenoshita Tadashi (no official reading for this name is given; other possible readings for the name include Masashi, Masaru, Akira, Makoto and more): Sodenoshita (袖の下) means 'bribery'. The last two characters (下正) almost look like fusei (不正）, 'dishonest'/'corruption'.
亜内武士 / Auchi Takeshi: The name was chosen to resemble his father's name in appearance. Taketsuchi (武土) VS Takeshi (武士).

ポラン・マスグレイブ / Polan Musgrave: Charanporan (ちゃらんぽらん) means 'haphazard'/'done on the spur of the moment'. Musgrave comes from the Sherlock Holmes short story The Musgrave Ritual.
チャラン・マスグレイブ: Charan Musgrave: Charanporan (ちゃらんぽらん) means 'haphazard'/'done on the spur of the moment'. Musgrave comes from the Sherlock Holmes short story The Musgrave Ritual.

Mamemomi might be from "memo" or "memoru" (Japanese-English fusion verb for "to write a memo"). He uses the term "mememomi memo" a few times during the case.

Decargo Mieterman also has another pun: Mieterman could come from "Mitta man", which in Japanese could mean either "man who saw it" or "saw it all".

Courtney's maiden name Simon could come from "Shimon", which could mean either "fingerprints" (referencing her forensics role) or "gate of death".

Dobinbough could also come from "bou", boy. His theme is called "Science Boy.

As a side note, if I was a localizer I'd call Elyder Meningen "Riley Badmann".

This is just a theory, since "Seishiro" is a semi-common Japanese name, but Seishirō Itagaki was the name of Japan's War Minister during World War II, who was hanged for war crimes. Considering this guy's (Seishirou Jigoku) last name is literally "Hell", they were probably going for a "Names To Run Away From Really Fast" thing with him, so this origin isn't out of the question.