I think it's hard to tell which Paxton sog is most popular. I think it's clear, though, that his 1964 debut album, Ramblin' Boy, has a good chunk of his most popular work. I put my favorites in bold

1. "A Job of Work" – 2:44
2. "A Rumblin' in the Land" – 2:59
3. "When Morning Breaks" – 2:55
4. "Daily News" – 2:17
5. "What Did You Learn in School Today?" – 1:44
6. "The Last Thing on My Mind" – 3:05
7. "Harper" – 2:52
8. "Fare Thee Well, Cisco" – 3:04
9. "I Can't Help But Wonder Where I'm Bound" – 3:41
10. "High Sheriff of Hazard" (Paxton, Traditional) – 2:10
11. "My Lady's a Wild Flying Dove" – 3:11
12. "Standing on the Edge of Town" – 1:43
13. "I'm Bound for the Mountains and the Sea" – 3:04
14. "Goin' to the Zoo" – 2:29
15. "Ramblin' Boy" – 3:59

I'd dare to say that almost all of his "greatest hits" are on that album. Two other favorites of mine, "The Marvelous Toy" and "Bottle of Wine," came out early in Paxton's career. He's still writing great songs, but most of his hits came out early.
-Joe-