The best way I found to implement Colemak on Windows is using registry remapping, but that messes up the Hebrew layout. To compensate, I've created an alternative Hebrew layout using MSKLC. When installed together with the registry remapping, it creates a regular Hebrew keyboard (normal Israeli mapping) alongside Colemak.
Caveat emptor. Not thoroughly tested, and not supported.
KBD HebCmkGr "Hebrew layout for registry-remapped Colemak"
COPYRIGHT "(c) 2012 Company"
COMPANY "Company"
LOCALENAME "he-IL"
LOCALEID "0000040d"
VERSION 1.0
SHIFTSTATE
0 //Column 4
1 //Column 5 : Shft
2 //Column 6 : Ctrl
6 //Column 7 : Ctrl Alt
7 //Column 8 : Shft Ctrl Alt
LAYOUT ;an extra '@' at the end is a dead key
//SC VK_ Cap 0 1 2 6 7
//-- ---- ---- ---- ---- ---- ---- ----
02 1 0 1 0021 -1 -1 -1 // DIGIT ONE, EXCLAMATION MARK, <none>, <none>, <none>
03 2 0 2 0040 -1 -1 -1 // DIGIT TWO, COMMERCIAL AT, <none>, <none>, <none>
04 3 0 3 0023 -1 20ac -1 // DIGIT THREE, NUMBER SIGN, <none>, EURO SIGN, <none>
05 4 0 4 0024 -1 20aa -1 // DIGIT FOUR, DOLLAR SIGN, <none>, NEW SHEQEL SIGN, <none>
06 5 0 5 0025 -1 00b0 -1 // DIGIT FIVE, PERCENT SIGN, <none>, DEGREE SIGN, <none>
07 6 0 6 005e -1 05ab -1 // DIGIT SIX, CIRCUMFLEX ACCENT, <none>, HEBREW ACCENT OLE, <none>
08 7 0 7 0026 -1 05bd -1 // DIGIT SEVEN, AMPERSAND, <none>, HEBREW POINT METEG *, <none>
09 8 0 8 002a -1 00d7 -1 // DIGIT EIGHT, ASTERISK, <none>, MULTIPLICATION SIGN, <none>
0a 9 0 9 0029 -1 200e -1 // DIGIT NINE, RIGHT PARENTHESIS, <none>, LEFT-TO-RIGHT MARK, <none>
0b 0 0 0 0028 -1 200f -1 // DIGIT ZERO, LEFT PARENTHESIS, <none>, RIGHT-TO-LEFT MARK, <none>
0c OEM_MINUS 0 002d 005f -1 05be -1 // HYPHEN-MINUS, LOW LINE, <none>, HEBREW PUNCTUATION MAQAF, <none>
0d OEM_PLUS 0 003d 002b -1 2013 -1 // EQUALS SIGN, PLUS SIGN, <none>, EN DASH, <none>
10 Q 1 002f Q -1 05c2 -1 // SOLIDUS, LATIN CAPITAL LETTER Q, <none>, HEBREW POINT SIN DOT, <none>
11 W 1 0027 W -1 05c1 -1 // APOSTROPHE, LATIN CAPITAL LETTER W, <none>, HEBREW POINT SHIN DOT, <none>
12 E 1 05dc E -1 05b8 -1 // HEBREW LETTER LAMED, LATIN CAPITAL LETTER E, <none>, HEBREW POINT QAMATS, <none>
13 R 1 05d3 R -1 05b3 -1 // HEBREW LETTER DALET, LATIN CAPITAL LETTER R, <none>, HEBREW POINT HATAF QAMATS, <none>
14 T 1 05db T -1 -1 -1 // HEBREW LETTER KAF, LATIN CAPITAL LETTER T, <none>, <none>, <none>
15 Y 1 05dd Y -1 05f0 -1 // HEBREW LETTER FINAL MEM, LATIN CAPITAL LETTER Y, <none>, HEBREW LIGATURE YIDDISH DOUBLE VAV, <none>
16 U 1 05df U -1 05b9 05ba // HEBREW LETTER FINAL NUN, LATIN CAPITAL LETTER U, <none>, HEBREW POINT HOLAM, HEBREW POINT HOLAM HASER FOR VAV
17 I 1 05da I -1 -1 -1 // HEBREW LETTER FINAL KAF, LATIN CAPITAL LETTER I, <none>, <none>, <none>
18 O 1 05e3 O -1 -1 -1 // HEBREW LETTER FINAL PE, LATIN CAPITAL LETTER O, <none>, <none>, <none>
19 P 1 05e8 P -1 05b7 -1 // HEBREW LETTER RESH, LATIN CAPITAL LETTER P, <none>, HEBREW POINT PATAH, <none>
1a OEM_4 0 005d 007d 200e 05b2 -1 // RIGHT SQUARE BRACKET, RIGHT CURLY BRACKET, LEFT-TO-RIGHT MARK, HEBREW POINT HATAF PATAH, <none>
1b OEM_6 0 005b 007b 200f 05bf -1 // LEFT SQUARE BRACKET, LEFT CURLY BRACKET, RIGHT-TO-LEFT MARK, HEBREW POINT RAFE, <none>
1e A 1 05e9 A -1 05b0 -1 // HEBREW LETTER SHIN, LATIN CAPITAL LETTER A, <none>, HEBREW POINT SHEVA, <none>
1f S 1 05d2 S -1 05bc -1 // HEBREW LETTER GIMEL, LATIN CAPITAL LETTER S, <none>, HEBREW POINT DAGESH OR MAPIQ (or shuruq), <none>
20 D 1 05e2 D -1 -1 -1 // HEBREW LETTER AYIN, LATIN CAPITAL LETTER D, <none>, <none>, <none>
21 F 1 05e7 F -1 -1 -1 // HEBREW LETTER QOF, LATIN CAPITAL LETTER F, <none>, <none>, <none>
22 G 1 05d0 G -1 05f1 -1 // HEBREW LETTER ALEF, LATIN CAPITAL LETTER G, <none>, HEBREW LIGATURE YIDDISH VAV YOD, <none>
23 H 1 05d9 H -1 05f2 -1 // HEBREW LETTER YOD, LATIN CAPITAL LETTER H, <none>, HEBREW LIGATURE YIDDISH DOUBLE YOD, <none>
24 J 1 05d8 J -1 05b4 200d // HEBREW LETTER TET, LATIN CAPITAL LETTER J, <none>, HEBREW POINT HIRIQ, ZERO WIDTH JOINER
25 K 1 05de K -1 -1 -1 // HEBREW LETTER MEM, LATIN CAPITAL LETTER K, <none>, <none>, <none>
26 L 1 05d5 L -1 201d 201c // HEBREW LETTER VAV, LATIN CAPITAL LETTER L, <none>, RIGHT DOUBLE QUOTATION MARK, LEFT DOUBLE QUOTATION MARK
27 OEM_1 SGCap 05e4 003a -1 201e 201d // HEBREW LETTER PE, COLON, <none>, DOUBLE LOW-9 QUOTATION MARK, RIGHT DOUBLE QUOTATION MARK
-1 -1 0 003b // SEMICOLON
28 OEM_7 SGCap 002c 0022 -1 05f4 -1 // COMMA, QUOTATION MARK, <none>, HEBREW PUNCTUATION GERSHAYIM, <none>
-1 -1 0 0027 // APOSTROPHE
29 OEM_3 0 003b 007e -1 05f3 -1 // SEMICOLON, TILDE, <none>, HEBREW PUNCTUATION GERESH, <none>
2b OEM_5 0 005c 007c 001c 05bb -1 // REVERSE SOLIDUS, VERTICAL LINE, INFORMATION SEPARATOR FOUR, HEBREW POINT QUBUTS, <none>
2c Z 1 05d6 Z -1 -1 -1 // HEBREW LETTER ZAYIN, LATIN CAPITAL LETTER Z, <none>, <none>, <none>
2d X 1 05e1 X -1 05b6 -1 // HEBREW LETTER SAMEKH, LATIN CAPITAL LETTER X, <none>, HEBREW POINT SEGOL, <none>
2e C 1 05d1 C -1 05b1 034f // HEBREW LETTER BET, LATIN CAPITAL LETTER C, <none>, HEBREW POINT HATAF SEGOL, COMBINING GRAPHEME JOINER
2f V 1 05d4 V -1 -1 -1 // HEBREW LETTER HE, LATIN CAPITAL LETTER V, <none>, <none>, <none>
30 B 1 05e0 B -1 -1 05c6 // HEBREW LETTER NUN, LATIN CAPITAL LETTER B, <none>, <none>, HEBREW PUNCTUATION NUN HAFUKHA
31 N 1 05d7 N -1 -1 200c // HEBREW LETTER HET, LATIN CAPITAL LETTER N, <none>, <none>, ZERO WIDTH NON-JOINER
32 M 1 05e6 M -1 05b5 -1 // HEBREW LETTER TSADI, LATIN CAPITAL LETTER M, <none>, HEBREW POINT TSERE, <none>
33 OEM_COMMA SGCap 05ea 003e -1 2019 2018 // HEBREW LETTER TAV, GREATER-THAN SIGN, <none>, RIGHT SINGLE QUOTATION MARK, LEFT SINGLE QUOTATION MARK
-1 -1 0 002c // COMMA
34 OEM_PERIOD SGCap 05e5 003c -1 201a 2019 // HEBREW LETTER FINAL TSADI, LESS-THAN SIGN, <none>, SINGLE LOW-9 QUOTATION MARK, RIGHT SINGLE QUOTATION MARK
-1 -1 0 002e // FULL STOP
35 OEM_2 SGCap 002e 003f -1 00f7 -1 // FULL STOP, QUESTION MARK, <none>, DIVISION SIGN, <none>
-1 -1 0 002f // SOLIDUS
39 SPACE 0 0020 0020 0020 -1 -1 // SPACE, SPACE, SPACE, <none>, <none>
56 OEM_102 0 005c 007c 001c -1 -1 // REVERSE SOLIDUS, VERTICAL LINE, INFORMATION SEPARATOR FOUR, <none>, <none>
53 DECIMAL 0 002e 002e -1 -1 -1 // FULL STOP, FULL STOP, , ,
KEYNAME
01 Esc
0e Backspace
0f Tab
1c Enter
1d Ctrl
2a Shift
36 "Right Shift"
37 "Num *"
38 Alt
39 Space
3a "Caps Lock"
3b F1
3c F2
3d F3
3e F4
3f F5
40 F6
41 F7
42 F8
43 F9
44 F10
45 Pause
46 "Scroll Lock"
47 "Num 7"
48 "Num 8"
49 "Num 9"
4a "Num -"
4b "Num 4"
4c "Num 5"
4d "Num 6"
4e "Num +"
4f "Num 1"
50 "Num 2"
51 "Num 3"
52 "Num 0"
53 "Num Del"
54 "Sys Req"
57 F11
58 F12
7c F13
7d F14
7e F15
7f F16
80 F17
81 F18
82 F19
83 F20
84 F21
85 F22
86 F23
87 F24
KEYNAME_EXT
1c "Num Enter"
1d "Right Ctrl"
35 "Num /"
37 "Prnt Scrn"
38 "Right Alt"
45 "Num Lock"
46 Break
47 Home
48 Up
49 "Page Up"
4b Left
4d Right
4f End
50 Down
51 "Page Down"
52 Insert
53 Delete
54 <00>
56 Help
5b "Left Windows"
5c "Right Windows"
5d Application
DESCRIPTIONS
0409 Hebrew layout for registry-remapped Colemak
LANGUAGENAMES
0409 Hebrew (Israel)
ENDKBD