13
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  1. Boss turns blind eye to knife user (4)
  2. Charge with first-degree larceny makes sense (4)
  3. Recite backwards about king computer worm (6)
  4. Start donning trousers, topless educators (5)
  5. Initial understanding negotiated, communist backs down (5)
  6. Boys have top notch territories (5)
  7. Neo, alternatively! (3)
  8. Look for turban head by telephone (4)
  9. Point to uneven axioms (3)
  10. First groom taken by wife-to-be to game (6)
  11. Your hearing time long ago (4)
  12. Spring quest starts before fall ends (5)
  13. In distress, comedian Louis punches hard (5)
  14. Warning for ultimate disobedience (4)
  15. Dress up a ship's surface (4)
  16. Tetris complicated for caretaker (6)

What are we listing?

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13
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I've arrived rather late to this party, but here are all but one of the answers others haven't already got, along with ones others have already got for convenience, credit given by initials. [EDITED to add:] MOehm figured out the last one (#3), which I'm sure I would never have got. So now we have the full list.

CHEF    wv        1. Boss turns blind eye to knife user (4)
FEEL              2. Charge with first-degree larceny makes sense (4)
DABBER            3. Recite backwards about king computer worm (6)
DEANS             4. Start donning trousers, topless educators (5)
UNDER         js  5. Initial understanding negotiated, communist backs down (5)
LANDS             6. Boys have top notch territories (5)
ONE        ok     7. Neo, alternatively! (3)
SEEK          js  8. Look for turban head by telephone (4)
AIM               9. Point to uneven axioms (3)
BRIDGE           10. First groom taken by wife-to-be to game (6)
YORE    wv       11. Your hearing time long ago (4)
QUELL            12. Spring quest starts before fall ends (5)
SOCKS         js 13. In distress, comedian Louis punches hard (5)
FORE    wv       14. Warning for ultimate disobedience (4)
DECK    wv ok js 15. Dress up a ship's surface (4)
SITTER  wv    js 16. Tetris complicated for caretaker (6)

And, to answer the final question, we are listing

CHEF FEEL D / ABBER DEAN / S UNDER LAND / S ONE SEE / K AIM BRIDGE / YORE Q / UELL S / OCKS FORE D / ECK SITTER

which is to say

Sheffield, Aberdeen, Sunderland, Swansea, Cambridge, York, Wells, Oxford, Exeter

which are

British cities

though whether there is some more specific link I haven't yet figured out. [EDITED to add:] In comments, OP says nothing more specific was intended.

Note: an earlier version of this answer said (obviously absurdly) that they were

English cities

because I'm a moron; thanks to the OP for politely pointing out my mistake in the comments.

The table above omits explanations of the cryptic-clue solutions, for the sake of brevity. Here they are:

CHEF     1. Boss turns blind eye to knife user (4)                     CHIEF without I
FEEL     2. Charge with first-degree larceny makes sense (4)           FEE + L(arceny)
DABBER   3. Recite backwards about king computer worm (6)              READ< around BB
DEANS    4. Start donning trousers, topless educators (5)              D(onning) + (j)EANS
UNDER    5. Initial understanding negotiated, communist backs down (5) U(nder...) N(eg...) + RED<
LANDS    6. Boys have top notch territories (5)                        LADS contains N(otch)
ONE      7. Neo, alternatively! (3)                                    anag. &lit
SEEK     8. Look for turban head by telephone (4)                      sounds like SIKH
AIM      9. Point to uneven axioms (3)                                 AxIoMs (un-even letters)
BRIDGE  10. First groom taken by wife-to-be to game (6)                G(room) in BRIDE
YORE    11. Your hearing time long ago (4)                             sounds like YOUR
QUELL   12. Spring quest starts before fall ends (5)                   QUE(st) + (fa)LL
SOCKS   13. In distress, comedian Louis punches hard (5)               CK in SOS
FORE    14. Warning for ultimate disobedience (4)                      FOR + (disobedienc)E
DECK    15. Dress up a ship's surface (4)                              double def
SITTER  16. Tetris complicated for caretaker (6)                       anag. of TETRIS

Relevant not-entirely-universal knowledge:

3. There's a singer called B B King. 7. As in The Matrix. 8. Sikhs wear turbans. 12. The word QUELL has a (rather obscure) meaning of "spring or fountain". 14. "Fore!" is a warning cry in the game of golf, meaning "look out, fast-moving golf ball heading your way".

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  • $\begingroup$ I had just got 6 and 10 but 13 was from js. $\endgroup$ – Weather Vane Feb 6 at 13:39
  • $\begingroup$ OK, I've un-credited you for that one. Thanks for your honesty :-). $\endgroup$ – Gareth McCaughan Feb 6 at 13:43
  • $\begingroup$ I guess that 3 is rot13(qnoore). $\endgroup$ – M Oehm Feb 6 at 13:43
  • $\begingroup$ Plausible as far as definition goes, but I don't understand the wordplay. What am I missing? $\endgroup$ – Gareth McCaughan Feb 6 at 13:44
  • $\begingroup$ ... Oh, duh. I see. $\endgroup$ – Gareth McCaughan Feb 6 at 13:44
4
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Partial solution

Chef    1. Boss turns blind eye to knife user (4)
        2. Charge with first-degree larceny makes sense (4)
        3. Recite backwards about king computer worm (6)
        4. Start donning trousers, topless educators (5)
        5. Initial understanding negotiated, communist backs down (5)
Lands   6. Boys have top notch territories (5)
        7. Neo, alternatively! (3)
        8. Look for turban head by telephone (4)
        9. Point to uneven axioms (3)
Bridge  10. First groom taken by wife-to-be to game (6)
Yore    11. Your hearing time long ago (4)
        12. Spring quest starts before fall ends (5)
        13. In distress, comedian Louis punches hard (5)
Fore    14. Warning for ultimate disobedience (4)
Deck    15. Dress up a ship's surface (4)
Sitter  16. Tetris complicated for caretaker (6)

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3
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  1. Initial understanding negotiated, communist backs down (5)

UNDER (Initials of understanding negotiated is UN, communist is RED but backwards is DER, down is under)

  1. Look for turban head by telephone (4)

SEEK (sounds like Sikh, means to look for)

  1. In distress, comedian Louis punches hard (5)

SOCKS (In SOS, Louis CK is a comedian, socking means punching)

  1. Dress up a ship's surface (4)

DECK (as in Deck the halls, and a ship's deck.)

  1. Tetris complicated for caretaker (6)

SITTER (anagram of tetris, short for babysitter)

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2
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Partial:

6: Boys have top notch territories (5)

TERRY (front of territories, boy name)

7: Neo, alternatively! (3)

ONE (anagram of neo)

15: Dress up a ship's surface (4)

DECK (dress up = deck, ship's surface = deck)

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