It's difficult to define an exact list for an artist like Neil Young, who has made a lot of very different albums, but my top ten Neil Young albums (excluding 'compilation' live albums such as Live Rust or Weld) is approximately as follows:
1. Rust Never Sleeps
2. After The Gold Rush
3. On The Beach
4. Everybody Knows This Is Nowhere
8. Harvest Moon
9. Ragged Glory
10. Tonight's The Night
I am fairly sure of my top three, but lower down the list the order does move around somewhat.
I'll summarise my thoughts while trying not to be too exhaustive. Rust Never Sleeps takes top spot as one of the things I most love about Neil Young's music is his ability to combine great acoustic and electric music, and this album captures it probably better than any other. plus it contains several of his absolute best songs (the two 'bookend' songs, Thrasher and Powderfinger being particularly outstanding).
Gold Rush has plenty of great tunes (including comparatively lesser known songs like Tell Me Why and Don't Let It Bring You Down as well as the title track and Southern Man) and yet is still somehow even greater than the sum of its parts. I can say the same about On The Beach, where I especially love the mellowed out feel of the second side.
Everybody Knows This Is Nowhere was his first great album, a bit like Rust in the sense that it has a really good combination of loud and quiet tracks. Harvest is probably his most overexposed album, so it's easy to forget how good it is, but it really is an excellent album, although Zuma is not too far behind for me - Cortez The Killer is one of his finest tracks, but there's plenty of other strong songs there too.
Next up come his albums from the late 1980s and early 1990s. Freedom is one of the most eclectic rock albums I've heard, and the disparate styles work surprisingly well together. Harvest Moon and Ragged Glory represent the two opposite ends of Neil's stylistic range, but I love both the gorgeous country-flavoured ballads of the former and the raucous hard rock songs of the latter.
I think Tonight's The Night is a bit overhyped in some sections of the music press (I've always liked the material from On The Beach more) but nonetheless it's still a fine listen and worthy of a top ten slot.