Which episodes of Detective Conan are canon? Which episodes of Detective Conan are canonical to the manga?

After watching the first ~20 episodes, I get the feeling that there are quite a lot of non-canon material so far.
Check this out. It lists all the essential episodes in the storyline! Here's a copy of the content from that site (as of November 2014) with formatting added:


1-5
10
11
18
21 (1st appearance of Yoko-chan (idol))
27
28
32
34
35
42
43
48/49 (absolute must)
54
57/58
68-70
76 (enter Kid)
77/78
81/82 (Minami)
96
100/101
112 (1st appearance of Kobayashi Sumiko (teacher))
116-118
121/122
128
129-131
132-134 (Kid, 134 only)
136/137
141/142
146/147 (Police Love Story #1)
153/154
156/157 (Police Love Story #2)
162
166-168
170-171 (Araide intro)
174
176-178
188-193
199/200
205/206
217/218
219
220-224
226/227 (Jodie Santemillion debut)
228/229
230/231
233/234
236/237
238/239
241/241
246/247
249/250
253/254
255/256
258/259 (Enter James Black)
263
264-265 (Eri)
266-268
269
271/272
277/278
279/280
284-293
297-298 (Eri)
299-300
301/302
304
307-311
316/317
323/324
329-330 (Black Organization, Haibara's parents)
331/332
333/334
335/336
338/339
340/341
343/344
345 (most critical to date)
356
358/359
361/362
381/382
385-387
390/391
394-396
398-399
400-402
406-408
418
425 (another jaw dropper)
426 (Ran)
429-430
431-432
435-436
437
445
446/447
449
457/458
462-465
469-470 (Kid)
472-473 (Toichi!!)
474 (Eri)
479 (2hr, Heiji &amp; Hakuba)
484-485
487 (Police Love Story #8, 1hr special)
489 (Eri)
490 (Shinichi VS Heiji for the 1st time, but they didn't know it)
491-504
505-506 (Eri)
507-508 (Eisuke knows C is S)
509-511 (Enter Okiya or should we say Bourbon?)
515 (Kaitou Kid) 
516-517 (Heiji &amp; Kazuha)
521-523 (Shinichi back and he's a killer)
528-529 (Eri solves another murder)
530-531 (Satou &amp; Takagi)
534-535 (Satou &amp; Takagi)
537-538 (Kid)
542-543 (Okiya helps solve case)
545-546 (a bit of Satou's past)
554-555 (Heiji &amp; Kazuha)
558-561 (Detective Koumei intro)
563-564 (Akai (or his twin) lives?)
568-569 (Shiratori's love)
573-574 (Heiji &amp; Kazuha)
579/580/581 (Black Organization, Okiya, "Akai")
583-585 (Shiratori/Kobayashi)
586-587 (Kid)
589-590 (Eri &amp; Kogoro)
592-593 (Ran)
608-609 (affects all couples)
610-613 (Heiji; "Hound of the Baskervilles")
616-621 (London case!!)
622-623 (Okiya)
624 (Shiratori/Chiba)
627-628 (Kid) 
646-647 (Sera intro)
648-650 (Sera, Shinichi)
651 (1hr SP: Conan VS Heiji)
652-655 (Heiji/Kazuha)
656-657 (Haibara/Sera/Okiya)
659-660 (Chiba/Miike)
667-668 (Amuro's 1st appearance)
671-674 (Amuro, Sera, Okiya)
675-676 (Black Organization hints, relates back to 671-674)
681-683 (Takagi/Satou)
684-685 (Okiya/Haibara)
689 (Eri/Kogoro)
690-691 (Okiya/Sera/Y Kudo)
699-700 (Haibara/Amuro)
701-704 (MYSTERY TRAIN CASE)
705-706 (Amuro)
710-711 (Heiji/Kazuha/Ohtaki/Heizo)
712-715 (Heiji/Kazuha/Ohtaki)
722-723 (Tanteidan, Amuro, Okiya) 
724-725 (Kid, Sera)
727-728 (Sera)
731-732 (Yumi/Miike/Takagi/Megure)
734 (Jodie/Bourbon/Vermouth) 
740-741 (Sera, Black Organization hints)
744-745 (Sera, Makoto)
746-747 (Sonoko/Makoto/Kid)
748-749 (Takagi/Sato) 
751-752 (Amuro; Takagi/Sato)
754-756 (Sera, Akai, Yamato/Uehara)
759-760 (Sera, 1st appearance of her younger sister (?))
763-764 (Heiji/Kazuha),
770-771 (Amuro//Eri)
772-773 (Shinichi/Ran)
779-783 (Black Organization/Bourbon/Jodie/Vermouth/Akai)
785-786 (Yumi/Haneda)
787-788 (Sera/mystery girl)
792-793 (mention of Rum, the case itself is not important)