Hard to pick one for each decade, so there will be long list here, feel free to skip the post if you wish. I'll do a a few for each decade up through the 50s, but from the 60s on it going to be more, which might not always be in order and some might be one-shots rather than series though, and I am sure I am forgetting stuff. Long running series may disappear off the list once they've been mentioned, but that doesn't mean they are not a favorite of a given decade, it's just trying to streamline in places, others will recur as they are absolute favorites of any era. Things like Lee Falk's Phantom and the Phantom Stranger might be skirting it too close to super-hero even though they are other genres, so I won't list them, but if you consider them non-super-hero it would be there as well.
30's1. Raymond's Flash Gordon
2. Caniff's Terry and the Pirates
3. Foster's Tarzan
4. Herge's Tintin
5. Segar's Popeye
6. Gould's Dick Tracy
40s1. Eisner's Spirit
2. Canniff's Terry and the Pirates
3. Herge's Tintin
4. Planet Comics
5. Walt Kelly's Pogo
5. Uncle Scrooge stories
50s1. Eisner's the Spirit
2. Piracy (really any of the EC stuff, Piracy is just my favorite of them)
3. Charles Schulz's Peanuts
4. Son of Sinbad (Kubert)
5. Canteen Kate (Matt Baker)
6. Sgt. Rock in Our Army at War
7. Uncle Scrooge
8. Toth's Zorro
60s1. Sgt. Rock in Our Army at War
2. Valerian
3. Witzend
4. Blazing Combat
5. His Name is Savage
6. Druillet's Lone Sloane
7. Bat Lash
8. Blueberry by Jean Giraud (Moebius)
9. Creepy
10. Eerie
11. Corto Maltese by George Pratt
12. Toth's Hot Wheels (I only have 1 issue but I so want the rest)
70s1. Savage Sword of Conan/Savage Tales
2. Conan the Barbarian
3. Kull
4. Warlord
5. Scooby Doo
6. Sgt. Rock
7. Kubert's Tarzan
8. Heavy Metal
9. Blackmark
10. Elfquest
11. Kubert's Tor
12. Ditko & Wood's Stalker
13. Chilling Adventures in Sorcery/Red Circle Sorcery
14. House of Mystery
15. House of Secrets
16. Losers in Our Fighting Forces
17. Unknown Soldier (plus Star Spangled War Stories)
18. Micronauts (if it counts as non-super-hero)
19. Red Sonja
20. Star Wars from Marvel
21. Unknown Worlds of Science Fiction
22. Warren's Spirit Magazine
23. Warren's 1984
24. The Horns of Elfland by Charles Vess
25. Alien adaptation by Goodwin & Simonson
26. First Kingdom by Jack Katz
27. Star * Reach
28. any Charlton horror book
29. Hot Stuf'
80s1. Usagi Yojimbo by Sakai
2. The Incal by Moebius/Jodo
3. Conan/SSOC
4. Sgt. Rock
5. Metamorphosis Odyssey/Dreadstar
6. John Sable, Freelance
7. Warlord
8. Maus by spiegleman
9. TMNT
10. Zot! by Scott McCloud
11. Epic Illustrated
12. Elric (series of minis through First)
13. Jonny Quest
14. Elfquest
15. DC's D&D comics (AD&D. Forgotten Realms, Dragonlance, etc.)
16. Calvin & Hobbes by Watterson
17. Bloom County by Breathed
18. Love and Rockets by Los Brothers Hernandez
19. Rocketeer by Stevens
20. V for Vendetta by Moore & Lloyd
21. Blackhawk by Evanier & Spiegle
22. Groo by Aargones & Evanier
23. DC's Star Trek
24. Kitchen Sink's Spirit & Spirit magazine
25. Alien Worlds
26. Alien Encounters
27. Mister X
29. A Distant Soil by Colleen Doran
30. Thieves World by Aspirin/Abbey & Tim Sale
31. Concrete by Paul Chadwick
32. Star Slammers by Simonson
33. Journey by William Messner-Loebs
34. Critters
35. Anything Goes
36. Dark Horse Presents
37. Attu by Sam Glanzman
38. Xenozoic Tales
39. Children of Fire by Corben
40. Den by Corben
41. Dalgoda
42. Echo of Futurepast
43. The Hobbit by Wenzel from Eclipse
44. Ms. Tree
45. Sandman by Gaimian
46. Rip in Time by Corben
47. 'Nam from Marvel
90s1. Bone
2. Uncle Scrooge (particularly the Gladstone launch, really any of the Gladstone Ducks)
3. Strangers in Paradise by Terry Moore
4. Leave it to Chance
5. Breed by Starlin
6. Castle Waiting by Linda Medley
7. Finder by Carla Speed McNeil
8. Hicksville by Dylan Horrocks
9. Usagi Yojimbo
10. Space Usagi
11. Strangehaven by Gary Spencer Milledge
12. Berlin by Jason Lutes
13. Hellboy (and all the Mignolaverse) by Mignola & friends
14.Scooby Doo (DC)
15. Planetary by Ellis/Cassaday
16. The Book of Ballads and Saga by Charles Vess
17. Clan Apis
18. Colonia by Jeff Nicholson
19. Sin City by Miller
20. Cheval Noir
21. Classics Illustrated (First Comics; especially #4 Sienkewicz's Moby Dick)
22. Tellos by DeZago & Wieringo
23. Frank Frazetta Fantasy Illustrated
24. Nocturnals by Brereton
25. Mickey Spillane's Mike Danger
26. Roland: Days of Wrath
27. Goldfish by Bendis
28. The Spirit: New Adventures from Kitchen Sink
2000-20101. Bone (+ Rose by Smith & Vess)
2. Usagi Yojimbo
3. Scooby Doo (DC)
4. Criminal by Ed Brubaker and Sean Phillips
5. Sleeper by Brubaker/Phillips
6. Planetary by Ellis/Cassaday
7. RASL by Jeff Smith
8. Spirit by Darwyn Cooke
9. Conan by Busiek & Nord
10, Sandwalk Adventures
11. Queen and Country by Rucka et. al
12. The Fall by Brubaker & Lutes
13. Sweet Tooth by Lemire
14. Dignifying Science or any of the science comics by Jim Ottoviani and company
15. Fear Agent by Remender & friends
16. Mouse Guard by David Petersen
17. Order of the Stick by Rich Burlew
18. PCR's Ring of the Nibelung
19. Fables
20. Rex Mundi
21. Powers by Bendis & Oeming
22. Northlanders
23. Grimoire
24. Metabarons by Jodo
25. Metal Hurlant revival from Humanoids
26. Torso by Bendis
27. Secret History (Archaia)
2010-present1. Usagi Yojimbo
2. Parker by Darwyn Cooke
3. Fatale by Brubaker/Phillips
4. The Fade Out by Brubaker/Phillips
5. Kill or Be Killed by Brubaker/Phillips
6. Reckless by Brubaker/Phillips
7. Pulp by Brubaker Phillips
8. Velvet by Brubaker/Epting
9. Lazarus by Rucka/Lark
10. Black Magick by Rucka/Lark
11.Stumptown by Rucka
12.Descender/Ascender by Lemire & Ngyuen
13. Trillium by Lemire
14. Southern Bastards by Aaron * firends
15. Autumnlands by Busiek et. al
16. Somethng is Killing the Children by James Tynion et. al
17. Department of Truth by James Tynion et. al
18. Injection by Warren Ellis
19. The Sixth Gun by Cullen Bunn et. al
20. Half Past Danger (and sequel) by Stephen Mooney
21. Saga by Vaughan and Staples
22. Five Ghosts
23. Black Beetle by Francavilla
24. Helheim/Brides of Helheim by Bunn et. al.
25. Gideon Falls by Lemire & Sorrentino
26. Folk Lords by Kindt
27. Frankenstein Alive, Alive by Wrightson
28. Invisible Kingdom by Wilson et. al.
29. Norse Mythology by PCR. Gaiman et. al
30. Ragnarok by Simonson
31. Red Sonja by Mark Russell
32. Wytches by Snyder & Jock
I am sure there will be more as I get through the backlog of stuff in my to read pile (lots of 80s indies in there for instance like Nexus, Grimjack, Ameircan Flagg, etc.) or as I finish series with holes in them and read them, but there's enough here to keep anyone interested in non-super-hero comics reading for a long time, and yes, these are all favorites I either return to regularly or intend to revisit again when I get the chance.
-M