I'd do them separately. It's a bit dependent on what kind of list you're making though, since you could count one path as DLC I guess.
This is what I have done regarding my Video Game Collection.
Nintendo 3DS Games:
1. Super Street Fighter IV: 3D Edition
2. Legend of Zelda Ocarina of Time 3D
3. Super Mario 3D Land
4. Sonic Generations
5. Mario Kart 7
6. The Sims 3
7. Super Pok?mon Rumble
8. Kid Icarus: Uprising
9. Mario Tennis Open
10. New Super Mario Bros. 2
11. Paper Mario Sticker Star
12. Luigi’s Mansion 2
13. Donkey Kong Country Returns 3D
14. Animal Crossing New Leaf
15. Mario and Luigi: Dream Team Bros.
16. Pok?mon X
17. Pok?mon Y
18. Harvest Moon 3D: A New Beginning
19. Sonic Lost World
20. Legend of Zelda: A Link Between Worlds
21. Scribblenaut’s Unlimited
22. Mario Party: Island Tour
23. Yoshi’s New Island
24. Mario Golf World Tour
25. Hometown Story
26. Fantasy Life
27. Kirby Triple Deluxe
28. Tomodachi Life
29. Pok?mon Omega Ruby
30. Pok?mon Alpha Sapphire
31. Legend of Zelda: Majora's Mask 3D
32. Puzzles and Dragons Z + Puzzles and Dragons: Super Mario Bros. Edition
33. Code Name: S.T.E.A.M
34. Harvest Moon 3D: The Lost Valley
35. Legend of Zelda: Tri-Force Heroes
36. Chibi-Robo! Zip Lash
37. Rodea the Sky Soldier
38. Story of Seasons
39. Hyrule Warriors Legends
40. Fire Emblem Fates: Birthright
41. Fire Emblem Fates: Conquest
42. Kirby: Planet Robobot