I find a paper containing new lists of cognates on PIE root level, and don't know such phenomena or rules are convincing or not, the list follows below:
1. The voiceless stop vs. voiced aspirated stop alternation3
1.1. *dʰrei̯k(ʰ)- vs. *dʰrei̯gʰ-: ‘hair, bristle’
1.2. *h₁eḱ(s)- vs. *h₁eǵʰ(s)-: ‘out’
1.3. *(h₂)kou̯s- vs. *gʰou̯s-: ‘hear, sound’
1.4. **h₁reu̯t- vs. *h₁reu̯dʰ-: ‘red’
1.5. *ḱ(e)rd- vs. *ǵʰ(e)rd-: ‘heart’
1.6. *kap- vs. *gʰabʰ-: ‘grab, take’
1.7. *kaput- vs. *k(a)ubʰut-: ‘head’
1.8. *ḱel-1 vs. *ǵʰel(h₂)-/*gʰel-1: ‘warm, bright, shine, yellow, green, blue, sun’
1.9. *ḱelb- vs. *ǵʰelb-/gʰelb-: ‘help’
1.10. *ḱer-2 vs. *gʰer-: ‘grow’
1.11 . *ḱe-/*ḱo- vs. *gʰe-/*gʰo-: ‘this, that’
1.12. *ko(m)- vs. **gʰo(m)-: ‘with, together’
1.13. *lei̯p-1 vs. *Hlei̯bʰ-: ‘smear, stick’
1.14. *lei̯t-1, *lei̯t(ʰ)-29 vs. *lai̯dʰ-: ‘be disgusted, suffer, hurt’
1.15. *lento-12 vs. *lendʰ-1: ‘flexible, fluid’
1.16. *mei̯k- vs. *mei̯gʰ-: ‘close the eyes’
1.17. *n̥ter- vs. *n̥dʰer-: ‘under, below’
1.18. *pel-9 vs. *bʰel-1: ‘white, shine, burn’
1.19. *per-2/*per-2B vs. *bʰer-1: ‘over, go over, carry over’
1.20. *pleu̯- vs. *bʰleu̯-: ‘run, flow, swim’
1.21 . *pleu̯k- vs. **pleu̯gʰ-: ‘fly’
1.22. *plou̯- vs. *b(ʰ)lou̯-: ‘flea’
1.23. *rep- vs. *rebʰ-: ‘grab, rip out, be taken, be furious’
1.24. *sek-2, *skei̯- vs. *segʰ-, **sgʰei̯-: ‘cut, separate’
1.25. *(s)keu̯p- vs. *(s)keu̯b(ʰ)-: ‘bundle, flock’
1.26. *telek- vs. *teleǵʰ-13: ‘hit’
1.27. *ters- vs. *dʰer-2: ‘dry’
1.28. *-tlom vs. *-dʰlom, *-trom vs. *-dʰrom: instrumental suffixes
1.29. *tragʰ- vs. *dʰ(e)ragʰ-: ‘pull, bring’
1.30. *u̯ekʷ- vs. *u̯egʷʰ-: ‘speak, speak solemnly’
2. The *l/*n alternation
2.1. *al-1, *ol- vs. *an-2, *on-: ‘this, that’
2.2. *mel-4 vs. *men(e)gʰ-: ‘much’
2.3. *pleu̯- vs. *pneu̯-: ‘flow, blow’
2.4. *-sleh₂ vs. *-sneh₂: object indicative suffixes
2.5. *su̯el- vs. *su̯en-: ‘sun’
2.6. *u̯el-2 vs. *u̯en-1/*u̯enH-: ‘want, love’
2.7. *u̯el-8 vs. *u̯en-2: ‘hurt, hit’
3. Co-occurrence of both alternations
3.1. *gal-2 vs. *gʰel- vs. *kel-6 vs. *kan-/*ḱan-: ‘call, cry, sing’
The data is from "Consonantal Alternations in Indo-European Roots: Diatopic and/or Diachronic Variants or Functional Mechanism?", published by "Journal of Indo-European Studies The 45 Vol., 2017"