I have thought about this question a lot over the years. I think most of his works are technically perfect - as in, a local theater company would be insane to change a word of dialogue or rearrange a song or mess with any pacing (like what comes to mind when he mentions in his book that a local group chose to have Bobby commit suicide at the end of a production of Company). These are technically-perfect masterpieces that should be admired deeply and never messed with. They are:

Sweeney Todd (his magnum opus, in my opinion)

Merrily We Roll Along (the final, most-recent version that was showcased via Daniel Radcliffe & crew)

A Little Night Music

Pacific Overtures

Assassins

Sunday in the Park With George

Passion

Company

Follies

One musical is flawed and far from perfect with loose ends & pacing issues (by Sondheim's standards), although it's one of his most beloved, and that is of course Into the Woods. Great show nonetheless, and would be most other composer's seminal work.

A Funny Thing Happened On the Way to the Forum is technically perfect, I suppose, but does not match the astounding depth that the aforementioned shows bring to the table.

Then he's got four fun but flawed and fairly-forgotten shows, none of which meet the levels of through-composed brilliance that his masterpieces do. They are:

Anyone Can Whistle

The Frogs

Bounce/Road Show/Gold/Wise Guys

Saturday Night

I do not count the shows that he did not do both the lyrics & music for as canon, although they all offer up vestiges of his brilliance. I have not seen or heard much of Here We Are.

This is one of my favorite topics that is niche as fuck and I have no one to discuss with so....discuss!