This morning at the bagel place the clerk said, "May I help who's next in line?"
I have two theories. One is that "who" is short for "whoever" (not "whomever," which would be a grammatical error which no bagel clerk would conceivably make).
The other theory is that the word "him" has been omitted before the word "who," thus: "May I help him who is next in line?"

On the other hand, the clerk didn't know if the person next in line was male or female, so actually "who" is short for "him or her who": "May I help him or her who is next in line?"
Or, in more modern, genderless English, "May I help them who is next in line?"
Opinions are solicited.
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This morning at the bagel place the clerk said, "May I help who's next in line?" I have two theories . . . . Opinions are solicited.

Mine is that the clerk had an incomplete understanding of English grammar.
I like what the clerk said better than your alternatives. Consider these usages from OED:
1728 Swift My Lady's Lament. 174 Find out who's master, who's man.
1783 London Chron. 22 Nov. 501/2 A box lobby Puppy comes in at halfprice, and immediately goes to the box-book to see who's there.
1823 J. F. Cooper Pioneers ii. xv. 223 Square yourself, youlubber,..and we'll soon know who's the better man.
1930 'J. J. Connington' Two Tickets Puzzle xiv. 222 There's nogreat trouble in guessing who's mixed up in the business-that's dead easy.
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This morning at the bagel place the clerk said, "May I help who's next in line?" I have two theories. ... in line?" Or, in more modern, genderless English, "May I help them who is next in line?" Opinions are solicited.

It's elliptical for "May I help the person who's next in line?", which is an attempt at a polite version of "Who's next (in line)?"

Adrian
This morning at the bagel place the clerk said, "May I help who's next in line?" I have two theories. ... in line?" Or, in more modern, genderless English, "May I help them who is next in line?" Opinions are solicited.

Next!

Skitt
Living in The Heart of the Bay
http://www.ci.hayward.ca.us/
This morning at the bagel place the clerk said, "May I help who's next in line?" I have two theories. ... in line?" Or, in more modern, genderless English, "May I help them who is next in line?" Opinions are solicited.

I would have expected "the next in line" rather than "who is" which sounds vaguely like a question.

Rob Bannister
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This morning at the bagel place the clerk said, "May ... have two theories . . . . Opinions are solicited.

Mine is that the clerk had an incomplete understanding of English grammar.

That is not often a requirement for a clerk at the bagel counter.

I wouldn't object to the usage, though. The clerk is showing rare initiative for a person in that capacity. Rather than disappear on his or her break when customers appear in line, stand and there stare vacantly at the people in line, or snarl out "Whadjawant?", the person is encouraging customers to do what they came to do: order a bagel.

I'll take good service over good grammar at the bagel shop any day.

Tony Cooper
Orlando, FL
This morning at the bagel place the clerk said, "May I help who's next in line?"

Maybe the clerk said "May I help? Who's next in line?" and you simply dismissed the rising inflections as Valley speech.

Richard Yates
This morning at the bagel place the clerk said, "May ... have two theories . . . . Opinions are solicited.

Mine is that the clerk had an incomplete understanding of English grammar.

Nevertheless, I've heard such statements with enough frequency that it sounds completely normal to me.
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