Here they are:
Top 100 City Pairs Worldwide by Monodirectional International & Domestic Scheduled Seats in 2007
Source: OAG Data
Ranking From To Seats in 2007
1 CTS HND 7,712,102
2 HND CTS 7,711,539
3 HND FUK 5,725,222
4 FUK HND 5,725,159
5 HKG TPE 4,917,314
6 TPE HKG 4,911,010
7 BCN MAD 3,913,125
8 MEL SYD 3,908,529
9 ITM HND 3,843,456
10 HND ITM 3,841,744
11 MAD BCN 3,836,165
12 CJU GMP 3,767,381
13 SYD MEL 3,762,664
14 GMP CJU 3,750,991
15 OKA HND 3,226,676
16 HND OKA 3,182,219
17 SDU CGH 3,156,240
18 CGH SDU 3,156,012
19 SHA PEK 3,131,150
20 PEK SHA 3,127,990
21 DEL BOM 3,110,331
22 BOM DEL 3,065,230
23 PVG HKG 2,858,173
24 HKG PVG 2,848,010
25 CPT JNB 2,768,900
26 JNB CPT 2,766,749
27 SYD BNE 2,641,318
28 BNE SYD 2,596,080
29 SUB CGK 2,325,126
30 CGK SUB 2,297,308
31 JFK LHR 2,101,896
32 LHR JFK 2,101,646
33 CGK SIN 2,062,437
34 BKK HKG 2,055,208
35 BKK SIN 2,028,065
36 SIN BKK 2,026,831
37 HKG BKK 2,018,942
38 SIN CGK 2,014,412
39 GMP PUS 1,992,702
40 PUS GMP 1,984,843
41 LIN FCO 1,931,477
42 FCO LIN 1,928,508
43 HIJ HND 1,917,487
44 HND HIJ 1,917,271
45 JNB DUR 1,904,084
46 DUR JNB 1,900,540
47 OGG HNL 1,846,044
48 HNL OGG 1,818,641
49 RUH JED 1,780,538
50 LAX LAS 1,752,962
51 MES CGK 1,750,099
52 JED RUH 1,733,519
53 CGK MES 1,720,773
54 DPS CGK 1,710,107
55 CAN PEK 1,703,930
56 LAS LAX 1,700,815
57 MCO ATL 1,694,276
58 ATL MCO 1,693,213
59 PEK CAN 1,684,718
60 KOJ HND 1,671,265
61 SFO LAX 1,656,136
62 HND KOJ 1,648,218
63 LAX SFO 1,628,033
64 LAS PHX 1,627,600
65 HKG SIN 1,604,452
66 SIN HKG 1,604,226
67 ORD LGA 1,604,038
68 HKT BKK 1,600,295
69 MEX MTY 1,595,215
70 LGA ORD 1,582,462
71 YYZ YUL 1,566,686
72 BLR BOM 1,563,296
73 PHX LAS 1,560,166
74 NRT TPE 1,551,656
75 TPE NRT 1,551,253
76 YUL YYZ 1,550,993
77 BOM BLR 1,544,211
78 ATL LGA 1,530,381
79 LGA ATL 1,527,377
80 MTY MEX 1,525,139
81 CGK DPS 1,520,511
82 CAN SHA 1,507,752
83 SHA CAN 1,507,315
84 GDL MEX 1,504,792
85 ICN NRT 1,494,858
86 NRT ICN 1,494,531
87 CTU PEK 1,489,713
88 BKK HKT 1,488,562
89 ORY TLS 1,485,326
90 NRT PVG 1,484,494
91 PVG NRT 1,484,466
92 TLS ORY 1,481,490
93 PEK CTU 1,476,765
94 HND KMJ 1,475,310
95 KMJ HND 1,464,217
96 HNL LIH 1,456,301
97 LIH HNL 1,443,504
98 MEX GDL 1,430,858
99 LAX JFK 1,429,216
100 NRT BKK 1,429,120