Comparison between the regular daytime version and the extended nighttime version of the music video.

When the song "Black Holse Sun" was released as a single, the music video at first was released in a pretty "unfinished" version which rather seemed to be crude - several special effects were missing, therefore some of the shots were used as "filler".
Later, the complete version of "Black Hole Sun" was given to the TV channels - the censors seemed to think that it was too precarious to show since some of the effects now looked pretty disturbing; as a result, the "finished" version was only shown during nighttime while the "unfinished" version was still aired during daytime (and therefore established itself as the "regular" version).

Runtime of both versions: 5:15 min

There's no difference in time!

General Remarks:
The backgrounds were slightly "polished" and almost all of them now offer clouds.

The band performs in front of dark purple clouds which move from north to south pretty fast. The nighttime-version shows the band in front of calm light blue clouds which move from east to west.
The nighttime-version does show the purple background a few times but never during the verses.
Sometimes the nighttime-version misses out on hills or grass.

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0:00 - 0:16
In the daytime-version, the first few shots are pretty static while the nighttime-version constantly fades these shots in and out.

0:13
The image of the sun looks more "diabolic".

0:14
The nighttime-version shows an image of a black hole. The daytime-version instead shows the previous shot a little longer.

0:26
The man's mouth corners were distorted.

0:28
The man's face was distorted. Additionally, the background was changed.

0:33
The grimace was distorted differently. Additionally, the background was changed.

1:03
The woman's face was distorted to a grimace.

1:12
CGI-cockroaches fly around the chandelier.

1:26
The call number "1-800 TRUTH" was cut out of the TV sequence by zooming closer to the image.

2:03
CGI-cockroaches attack a boy who's floundering on the floor.

2:06
2 boys are attacked by CGI-cockroaches.

2:07
At this point they used an alternative take with a dancing girl. In the daytime-version you see the old woman on the swing set.

2:10
The girl in the ballet appearel was digitally added to this scene.

2:29
In the daytime-version you see the young woman while in the nighttime-version you see the black hole.

2:34
Ditto.

2:47
The woman now has a CGI-chameleon-like tounge that hisses.

2:49
They added a CGI-butterfly. The woman catches it with her tongue. Some of the shots were mirrored. The last shot was exchanged with the shot of the girl with the braces because the daytime-version does not have the butterfly.

2:53
A shot of the black hole was altered.

2:54
The shot of the jubilant crowd who are sucked up by the black hole was altered. Additionally, the shot of the screaming girl with the braces was replaced by a shot of a woman with an eggbeater. The latter does not appear in the nighttime-version.

3:35
The face of the woman was distorted to a grimace. Additionally, the background was altered.

3:47
In the daytime-version you see the band while in the nighttime-version oyu see the "chandelier-people".

4:12
The background of the house was altered (now seems to fit a little better).

4:16
The man's face was distorted to a grimace.

4:17
The dog's face was distorted as well. In the daytime-version you instead see the man's face from the previous shot a little longer.

4:24
Wobbly floating stuff comes out of the buggy.

4:28
This weird stuff spreads out. In the daytime-version you instead see the drummer.

4:41
The woman's grimace looks different.

4:57
In the daytime version you see more of the band while in the nighttime-version some more people are sucked into the black hole.

5:13
In the daytime-version the video ends with a shot of the bass-player while in the nighttime-version it ends with a shot of the black hole.

Thanks to Reeze who made this report possible.