Pass, pass by

Both are correct. You'll see (hear) "pass by" a lot, but "by" is unnecessary.

In some contexts to pass means simply to move past but pass by can mean to move past without being noticed or acted upon. A year passed could mean simply that a year elapsed, without any implication, but a year passed by could mean that a year elapsed during which nothing important happened, or was done by someone.

I agree with what you're saying about subtle connotation, but that distinction is often overlooked in everyday speech.

For example, people will often say "a year passed by," without insinuating or implying anything beyond "passed."