I've seen all of the Simpsons episodes and I've noticed that, on reruns, sometimes very small bits of scenes are cut out. This happens infrequently so I'm assuming it's not to allow for more commercial time. What would be the reason for these omissions?

Actually, it is to allow for more commercial time.

Sometimes they cut out useless parts, but I hate it when they cut out the brilliant parts. The one I saw today, the episode "You Only Move Twice," cut out one of my favorite jokes:

Homer: [carrying coffee cup] Uh... you have any sugar around here?
Hank Scorpio: [fumbles in his pockets, takes out a few handfuls of sugar] Here you go. Sorry it's not in packets.

The rest is cut:
Hank Scorpio: Want some cream?
Homer: Uhhhh... I... no.

https://www.simpsonsarchive.com/episodes/3F23.html

By the way, it's spelled "D'oh!"

Yes, people who are even bigger fans than you or I have put together a list of all the scenes that were cut in syndication:
https://web.archive.org/web/20020807224203/http://www.snpp.com/episodes/scg.html