First, I want to post a bibliography of R. Margulies's works and then I shall discuss some biogrpahical details in the next post. This bibliography is not a scientific one in that I do not attempt to list every edition. Rather, I am listing just the works and some bibliogrpahical information as I see fit. Most of this information comes from Naftali Ben Menachem's bibliogprahy of R. Margulies's books which was printed in Sefer Margolious.
1) Toldot Adam (Lemberg 1912) on R. Shmuel Edels
2) Kav Besamim (Lemberg 1913) 102 notes on Tosefot
3) Drush l'yom 'alot 'al kesi moshlim 'adonanu haKeiser Karal haRishon (Lemberg 1918)
4) Kavi Ohr (Lemberg, 1921) laws pertianing to Israel as well as articles on history, including yesod hamishna among others
5) Yesod HaMishna V'Arikachto (Lemberg, 1933) on the creation of the Mishna
6) Sefer Hassidim with his notes (multiple printings)
7) Tolodot Rabenu Hayyim ben Atar (Lemberg, 1925), biography on the Ohr Hayyim includes the notes of R. Meir Dan Plotzki (Kli Hemdah)
8) Ohr Meir (Lemberg, 1926), biography of R. Meir from Perlmishiya
9) Margenuta d'Reb Meir (Lemberg, 1926), sayings of the above R. Meir
10) Shealot u'Teshuvot min HaShamyim, R. Margulies's extensive notes on the teshuvot as well as a comprehensive introduction discussing Torah lo' Bashmyim and other related topics (multiple printings)
11) Yalkut Margolious ([Lemberg], 1927), derashot of R. Margulies
12) Imrei Kodesh haShalem (Lemberg, 1928)
13) Vikuach Rabbanu Yehiel m'Paris (Lemberg, 1928), with biography of R. Yehiel
14) Shemot v'Kinuim B'Talmud, discussing names in the Talmud, including when two names started, (multiple printings)
15) Helulua d'Tzadika (Lemberg 1929), lifespan and death dates of Tzadikim
16) Vikuach HaRamban (Lemberg, 1928)
17) Yalkut Peninim (Lemberg, 1929), derashot
18) Butzna d'Nehora HaShalem (Lemberg, 1930), about R. Barukh of Metzerich
19) Gevurot Ari (Lemberg, 1930), biography of R. Leib Srhson
20) Toldot Rabbenu Avrohom Mimoni, biography of Rambam's son, (multiple printings)
21) Rishimah (Lemberg, 193-) list of books in his bookstore
22) Mekor Barukh (Lemberg, 1931), biography of R. Barukh of Metzerich and other historical documents
23) Shem Olam, to reveal the anonymous people in hazal (multiple printings)
24) HaModiah journal
25) Nefesh Hayyia, on Shulchan Orakh multiple printings
26) Hagadah shel Pesach (Tel Aviv, 1937)
27) Shichot Chakhamim
28) Mekor haBerakha discussing blessing and why and when before one does something (recently reprinted)
29) Zohar with his extensive notes (multiple printings)
30) Sibah hisnaguto discussing R. Emden/R. Eybeschitz controversy (very controversial Scholem wrote a pamphelet against this) Tel Aviv 1941
31) Reb Saul Levin M'Ziaf haSefer Besamim Rosh, in Aresehet 1944
32) Malechi Elyon on angels in Hazel (multiple printings)
33) Ollalot various articles (multiple printings)
34) Tikunei Zohar notes, multiple printings
35) Sefer haBahir same as above
36) Zohar Hadash same
37) L'Toldot Anshei Shem b'Lvov, Jerusalem 1952
38) Milchmot HaShem (R. Avrohom ben HaRambam) (including the biography on him) (multiple printings)
39) haRambam v'Hazohar now reprinted in Penini Margolios
40) Sha'ari Zohar collecting relvant passages from the Zohar to Hazal (multiple printings)
41) Margolios HaYam on Sanhedrin (multiple printings)
42) Divrarim b'Itam dershot
43) L'Heker haMisparam beTalmud, Sinai 44
44) Tzioyunim Bibliographim a comprehensive biobibliography in Areshet 1-2,4
45) Tziyunim l'Ha'arot l'Seder haDorot, Sinai 46
46) HaMikrah v'Hamesorah multiple printings
47) Mekharim b'Darkei haTalmud v'Hidosov multiple printings
1) Toldot Adam (Lemberg 1912) on R. Shmuel Edels
2) Kav Besamim (Lemberg 1913) 102 notes on Tosefot
3) Drush l'yom 'alot 'al kesi moshlim 'adonanu haKeiser Karal haRishon (Lemberg 1918)
4) Kavi Ohr (Lemberg, 1921) laws pertianing to Israel as well as articles on history, including yesod hamishna among others
5) Yesod HaMishna V'Arikachto (Lemberg, 1933) on the creation of the Mishna
6) Sefer Hassidim with his notes (multiple printings)
7) Tolodot Rabenu Hayyim ben Atar (Lemberg, 1925), biography on the Ohr Hayyim includes the notes of R. Meir Dan Plotzki (Kli Hemdah)
8) Ohr Meir (Lemberg, 1926), biography of R. Meir from Perlmishiya
9) Margenuta d'Reb Meir (Lemberg, 1926), sayings of the above R. Meir
10) Shealot u'Teshuvot min HaShamyim, R. Margulies's extensive notes on the teshuvot as well as a comprehensive introduction discussing Torah lo' Bashmyim and other related topics (multiple printings)
11) Yalkut Margolious ([Lemberg], 1927), derashot of R. Margulies
12) Imrei Kodesh haShalem (Lemberg, 1928)
13) Vikuach Rabbanu Yehiel m'Paris (Lemberg, 1928), with biography of R. Yehiel
14) Shemot v'Kinuim B'Talmud, discussing names in the Talmud, including when two names started, (multiple printings)
15) Helulua d'Tzadika (Lemberg 1929), lifespan and death dates of Tzadikim
16) Vikuach HaRamban (Lemberg, 1928)
17) Yalkut Peninim (Lemberg, 1929), derashot
18) Butzna d'Nehora HaShalem (Lemberg, 1930), about R. Barukh of Metzerich
19) Gevurot Ari (Lemberg, 1930), biography of R. Leib Srhson
20) Toldot Rabbenu Avrohom Mimoni, biography of Rambam's son, (multiple printings)
21) Rishimah (Lemberg, 193-) list of books in his bookstore
22) Mekor Barukh (Lemberg, 1931), biography of R. Barukh of Metzerich and other historical documents
23) Shem Olam, to reveal the anonymous people in hazal (multiple printings)
24) HaModiah journal
25) Nefesh Hayyia, on Shulchan Orakh multiple printings
26) Hagadah shel Pesach (Tel Aviv, 1937)
27) Shichot Chakhamim
28) Mekor haBerakha discussing blessing and why and when before one does something (recently reprinted)
29) Zohar with his extensive notes (multiple printings)
30) Sibah hisnaguto discussing R. Emden/R. Eybeschitz controversy (very controversial Scholem wrote a pamphelet against this) Tel Aviv 1941
31) Reb Saul Levin M'Ziaf haSefer Besamim Rosh, in Aresehet 1944
32) Malechi Elyon on angels in Hazel (multiple printings)
33) Ollalot various articles (multiple printings)
34) Tikunei Zohar notes, multiple printings
35) Sefer haBahir same as above
36) Zohar Hadash same
37) L'Toldot Anshei Shem b'Lvov, Jerusalem 1952
38) Milchmot HaShem (R. Avrohom ben HaRambam) (including the biography on him) (multiple printings)
39) haRambam v'Hazohar now reprinted in Penini Margolios
40) Sha'ari Zohar collecting relvant passages from the Zohar to Hazal (multiple printings)
41) Margolios HaYam on Sanhedrin (multiple printings)
42) Divrarim b'Itam dershot
43) L'Heker haMisparam beTalmud, Sinai 44
44) Tzioyunim Bibliographim a comprehensive biobibliography in Areshet 1-2,4
45) Tziyunim l'Ha'arot l'Seder haDorot, Sinai 46
46) HaMikrah v'Hamesorah multiple printings
47) Mekharim b'Darkei haTalmud v'Hidosov multiple printings