Each episode has their accompanying link and time stamp(s), unless otherwise noted. There are a couple important notes after the listing.
Season 1
#5 - Rupert and Bill in Gameland -
https://www.youtube.com/watch?v=gM43nQNy8ts (Bill, Dust - 1:50)
#7 - Rupert and the Knight -
https://www.youtube.com/watch?v=XNJLAtBRP98 (Bill, Cold - 2:44 & 2:56)
#11 - Rupert and the Twilight Fan -
https://www.youtube.com/watch?v=azW2lPw6Lco (Rupert & Bodkin, Feathers - 11:17-11:27)
Season 2
#14 - Rupert and the Temple Ruins -
https://www.youtube.com/watch?v=oE4UcxdQkpQ
(Edward, Dust - 15:02 & 19:08)
#17 - Rupert in Timeland -
https://www.youtube.com/watch?v=Vgdpb_uBDOA (Podgy & Rupert, Pepper - 4:06)
#24 - Rupert and the Lamp -
https://www.youtube.com/watch?v=P07qi-7mb8Y (Bill, Cloud (or "cotton wool" as he calls it) - 18:32, 18:40 & 19:03)
#25 - Rupert and the Firebird -
https://www.youtube.com/watch?v=f5K08V5Hg7Y (Firebird, Illness - 15:49)
Season 3
#29 - Rupert and the Dragon Race (already in archives)
#31 - Rupert and Ottoline -
https://www.youtube.com/watch?v=3JvtBuECML4 (Razor, Flour - 10:29, 11:22, 11:31, 11:36, 11:38, 13:03, 15:05 & 18:46)
Season 4
#45 - Rupert in Dreamland -
https://www.youtube.com/watch?v=OJR6GAsP_9E (Giant pickle, Pepper - 20:28)
#46 - Rupert's Roman Adventure -
https://www.youtube.com/watch?v=ku7xaGC5Ssw (Bill, Dust - 3:06)
#47 - Rupert in Mirrorland -
https://www.youtube.com/watch?v=Js1NNSmTf08 (Bill, Illness - 2:49, 7:34 & 7:59)
Season 5
#57 - Rupert and the Crystal Ball -
Rupert | Rupert and The Crystal Ball - Ep. 56 by BruceRheyr8515 - Dailymotion (Rupert, Dust - 14:58-15:11)
#58 - Rupert and the Sun Bandit -
Rupert | Rupert and The Sun Bandit - Ep. 57 by JoshuaElena4800 - Dailymotion (Mr. Bear, Illness - 2:26
Mrs. Bear, Illness - 3:27 & 10:39)
Notes:#1: Eps. #5, #7, #14, #17, #24, #25, #31, #57 and #58 have the wrong episode number on their respective web pages.
#2: I need confirmation on another episode:
#64 - Rupert and the Dragon Festival. There is a scene where a dragon breathes like a build-up and possibly sneezes from soot, but I am not sure. It is at 2:45 on this video:
Rupert | Rupert and the Dragon Festival - Ep. 62 by HubertRobert3825 - Dailymotion.