TOM

The six words could each be defined by DASH.  Treating each as a dash, the three rows became -/—/–, which, in MORSE CODE (17d) spells TOM.  Rearrangements of CAT were to be excluded from clues.

(In Memoriam our tom, Dash, killed by two dogs, 6 September, 2013)

Across

3              CONFOUND; con found (DASH)

11           ONUS; on(c)us

12           DEER; de(F)er; moo(T CA)se => moose

13           CREMASTERS; re m in casters

14           AUSTER; A (0)ust + re (rev.); Paul A; ou(TCA)st => oust

15           OORIAL; la I roo (all rev.)

16           NEIF; NE if; dire(CT A)ction => direction

17           MENU; men U; Cho(CTA)w => chow

19           ESTH; 2 mngs.

20           OUTDO; out do

22           SPIKY; I k in spy; (TAC)k => k

24           BLOW; B low (DASH)

25           RUSH; H for T in rust (DASH)

26           LONG; n in (s)log (DASH)

27           ESTEEM; (be)es teem

28           I SAY; ISA ¥

32           FARE; f are

34           TEEN; NEET (rev.)

36           COOS; coos(in)

37           YUAN; yu(L)an

39           SCOUTHER; scout her

40           SLOB; bols(hie) (rev.)

41           DELI; Deli(us)

42           FEES; f + see (rev.); f(ACT) => f

43           HYPHEN; hyp hen (DASH)

44           SPRINT; r in spin t (DASH)

Down

1              ROMANO-BRITISH; anag; (ACT)ion => ion

2              ON CUE; u in once; L(ACT)ate => late

3              CURSITOR; anag. + R; (TAC)tics => tics

4              NAME; am in NE

5              FLARE-OUT; are(a) in flout

6              OPSONISE; anag.

7              UNTO; (p)unto

8              DERISION; R I in noised (rev.); (TAC)it => it

9              RESAT; Taser (rev.)

10           ORAL HYGIENIST; anag; fl(AT-C)ap => flap

17           MORSE CODE; S in more cod E

18           USHERSHIP; us hership

21           ULES; (g)ules

23           KNAR; k N a R; (TAC)k => k

29           AESOP; sea (rev.) + op

30           ROUEN; roué n; he(CTA)re => here

31           ROTLS; L in rots

33           AUREI; ure in A1

35           EELY; (s)eely

38           AMEN; (r)amen