Hi, I found these links:

http://www.minilps.net/best-of-list/japrocksampler-julian-list-006

http://www.minilps.net/best-of-list/krautrocksampler-top-list-008

... but I don't know if these lists are correct, or eligible, or anything. I send it here just in case.

Well, I copy-paste the lists at least:
Japrocksampler:

001.SF-301 - Flower Travellin' Band - Satori (1971 / 2004)
002.SF-305 - Speed, Glue + Shinki - Eve (1971 / 2004)
003.Les Rallizes Denudés - Heavier than a Death in the Family
004.Far East Family Band - Parallel World
005.PRCD-5165 - J.A. Caesar (Seazer) - Kokkyou Junreika (1973 / 2006)
006.Love Live Life - Lowe Will Make a Better You
007.Masahiko Satoh & Soundbreakers - Amalgamation
008.Geino Yamashirogumi - Osorezan
009.SWAX-502 - Kosugi, Takehisa - Catch-Wave (1975 / 2002)
010.PCD-1465 - J.A. Caesar (Seazer) - Jashumon (1972 / 1999)
011.Far Out - Nihonjin
012.Les Rallizes Denudés - Blind Baby Has Its Mothers Eyes
013.Tokyo Kid Brothers - Throw away the books, we´re going out in the streets
014.Far East Family Band - Nipponjin
015.SF-306 - Speed, Glue + Shinki - Speed, Glue and Shinki (1972 / 2004)
016.People - Ceremony _ Buddha meets rock
017.ISCP-1151 - Blues Creation - Demon and Eleven Children ( ? / ? )
018.SF-302 - Flower Travellin' Band - Made In Japan (1972 / 2004)
019.Karuna Khyal - Alomoni 1985
020.Les Rallizes Denudés - Flightless Bird (Yodo-go-a-go-go)
021.Masahiko Satoh & New Herd Orchestra - Yamatai-Fu
022.ISCP-1141 - Magical Power Mako - Magical Power (1974) ( ? / ? )
023.FJSP51 - Taj Mahal Travellers - Live Stockholm July 1971 ( ? / 2008)
024.ISCP-1143 - Magical Power Mako - Jump ( ? / ? )
025.FJSP-55 - Kawachi, Kuni & Friends - Kirikyogen (1970 / 2008)
026.Brast Burn - Debon
027.Akira Ishikawa & Count Buffaloes - Uganda
028.ISCP-1116 - Flower Travellin' Band - Anywhere (1970 / ? )
029.PRCD-5166 - J.A. Caesar (Seazer) - Shin Toku Maru (1974 / 2006)
030.SWAX-115 - Gedo - Gedo ( ? / 2002)
031.Les Rallizes Denudés - December´s Black Children
032.Datetenryu - Unto 1971
033.East Bionic Symphonia - East Bionic Symphonia
034.Stomu Yamashita & Masahiko Satoh - Metempsychosis
035.SWAX-501 - Taj Mahal Travellers - July 15 1972 ( ? / 2006)
036.Toshi Ichiyanagi - Opera inspired by te work o Tadanori Yoko´o
037.PCD-1463 - Taj Mahal Travellers - August 1974 ( ? / 1998)
038.Seishokki - Organs of Blue Eclipse (1975-77)
039.Joji Yasa - Music for Theatrical Drama
040.Group Ongaku - Music of Group Ongaku
041.Far East Famiy Band - The Cave Down to Earth
042.TOCT-25104 - Jacks (The) - Vacant World ( ? / 2003)
043.PCD-18516/7 - 3/3 - Sanbun no san (1975 / 2007)
044.Blues Creation - Live
045.FLPB-001 - Various Artists - Genya Concert (1971 / 2003)
046.Toshi Ichiyanagi / Michael Ranta / Takehisa Kosugi - Improvisation Sept. 1975
047.Itsutsu no Akai Fusen - Flight 1&2
048.Maru Sankaku Shikaku - Complete Works (1970-73)
049.UPCH-20015 - Yoninbayashi - Isshoku Sokuhatsu ( ? / 2007)
050.PCD-1532 - Helpful Soul (The) - First Album ( ? / 1996)


Krautrocksampler:

1. Amon Düül "Paradieswärts Düül" (1970)
2. Amon Düül II "Phallus Dei" (1969)
3. Amon Düül II "Yeti" (1970)
4. Amon Düül II "Carnival in Babylon" (1972)
5. Amon Düül II "Wolf City" (1972)
6. Ash Ra Tempel "Ash Ra Tempel" (1971)
7. Ash Ra Tempel "Schwingungen" (1972)
8. Timothy Leary & Ash Ra Tempel "Seven Up" (1973)
9. Ash Ra Tempel "Join Inn" (1973)
10. Can "Monster Movie" (1969)
11. Can "Soundtracks" (1970)
12. Can "Tago Mago" (1971)
13. Can "Ege Bamyasi" (1972)
14. Can "Delay" 1968 (1981)
15. Cluster "Cluster II" (1972)
16. Cluster "Zuckerzeit" (1974)
17. Cluster "Sowiesoso" (1996)
18. Tony Conrad with Faust "Outside the Dream Syndicate" (1972)
19. The Cosmic Jokers "The Cosmic Jokers" (1973)
20. The Cosmic Jokers "Galactic Supermarket" (1974)
21. The Cosmic Jokers "Planeten Sit-In" (1974)
22. The Cosmic Jokers "Sci-Fi Party" (1974)
23. Sternenmädchen & Cosmic Jokers "Gilles Zeitschiff" (1974)
24. Faust "Faust" (1971)
25. Faust "So Far" (1972)
26. Faust "The Faust Tapes" (1973)
27. Faust "Faust IV" (1974)
28. Sergius Golowin "Lord Krishna von Goloka" (1973)
29.Guru Guru "UFO" (1970)
30. Harmonia "Musik von Harmonia" (1974)
31. Harmonia "Deluxe" (1975)
32. Kraftwerk "Kraftwerk" (1972)
33. La Düsseldorf "La Düsseldorf" (1976)
34. La Düsseldorf "Viva" (1978)
35. Moebius & Plank "Rastakraut Pasta"
36. Neu! "Neu!" (1972)
37. Neu! "Neu! 2" (1973)
38. Neu! "Neu! '75" (1975)
39. Popol Vuh "Affenstunde" (1970)
40. Popol Vuh "In den Gärten Pharaos" (1971)
41. Popol Vuh "Einsjäger & Siebenjäger" (1974)
42. Popol Vuh "Hosianna Mantra" (1972)
43. Tangerine Dream "Electronic Meditation" (1970)
44. Tangerine Dream "Alpha Centauri" (1971)
45. Tangerine Dream "Atem" (1973)
46. Tangerine Dream "Zeit" (1972)
47. Klaus Schulze "Irrlicht" (1972)
48. Klaus Schulze "Blackdance" (1974)
49. Walter Wegmüller "Tarot" (1973)
50. Witthüser & Westrupp "Trips und Träume" (1971)

I have no idea about the eligibility. But on another note, I recently got into the album Faust IV, so I want to check out some more krautrock. What albums should I get from that list (the only other one I've heard is Tago Mago, which I thought was good but flawed).

Hi Jackson, just my personal Krautrock list;
Can´s Tago Mago is a groundbreaking album, but certainly not their most accesible one. Maybe you should start with Ege Bamyasi (my favourite), Future Days or Soundtracks. Although the latter one is kinda uneven, it has some of the band´s best songs on it.
Amon Duül: Tanz Der Lemminge
Kraftwerk: Autobahn, Die Mensch Machine
Cluster: Zuckerzeit
Cosmic Jokers: Cosmic Jokers
Faust: So Far
A.R. & The Machines: Die Grüne Reise, Echo
Ashra Tempel: Schwingungen, Seven Up
Neu!: Neu, Neu 2
Harmonia: Deluxe
Brainticket: Cottonwoodhill
La Düsseldorf-La Düsseldorf
Klaus Schulze: Time Wind
Early Tangerine Dream is an acquired taste, with long monotonous drones. Easier to digest are later albums like Ricochet and Rubycon. All in all, when listening to Krautrock albums you should be prepared for brilliant moments interspersed with pointless noodling.
After you´ve checked out all these (and liked some), proceed to The Faust Tapes.

Thanks! I'm going to go with Future Days, Faust (their first self-titled album), Neu!, and Die Mensch Machine first, then move on to some of the more obscure picks (not that anything in this genre isn't obscure. I can already tell I'm going to find a lot of gems in this genre.