0 Note normal sky colour.
1 Place a part-filled chest [under a glass roof] so that you can still see the sky in the background while the chest inventory view is open.
2 Hover over an empty slot in the chest, then move the mouse to hover over a slot with items in it.
3 Sky color changes from darkened to extra-darkened as you swap from a full to an empty slot and back again.
This is a pretty harmless glitch, but I don't see why where you hover the mouse should affect the sky color at all. The glass ceiling part may be optional, but that's the setup under which I see this problem. Screengrabs can be made available if needed.
Update: description clarified. There's three states; normal sky, darkened sky (clearly an intentional background fading as part of the UI), and extra-dark.
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Screenshot please?
Since the initial report I've logged out and in again, and now upgraded to 1.4.4pre as well, and I can no longer reproduce it either. Please close for now, and I'll reopen and add screenshots if I can provoke it again.

Closed.
As you see, the sky is faded from its normal colour in both pictures, but it's lighter in one and darker in the other, depending on whether you're hovering the mouse over an item in the inventory or part of the light grey 'frame' window texture.
I have reproduced this in similar circumstances in 1.4.6, so it's an intermittent issue that is still present. I still can't quite do it on demand, but I have screengrabs taken mid-morning facing towards the sun which show the problem. Hovering the mouse over empty slots or other areas of whitespace in the Inventory window is a trigger. (NB reproduced this time using the 'E' Inventory window, not an open chest) Move the mouse over a slot with an item in it, and the colour changes back again. Please reopen. Thx. Screengrabs attached.
Reopened.
Additional data - seems to apply when the sun is on-screen. Visible but behind a cloud counts as on-screen. Even more, it's the leading and trailing corners of the sun that are the trigger area. So if you have just the correct corners visible, you can trigger it or prevent it.
Today I discovered that maps also misbehave in almost the same way. Hover the pointer over one item in the inventory or a chest, and you get one color, non-items give the other.
confirmed for 13w09c
I think it also depends on what biome you're in.

For example ?
no, I was wrong, it seems to just always happen. Only with a chest though, and hovering over an item only changes the brightness of signs for me, not the sky. But if you want too see the difference between a not dark and a dark sky:
-place a chest
-open it while looking at the sky
-press esc and e very fast
-you'll see the difference

@Jesper the End: Can confirm your procedure, but that is a different issue as this ticket.
This ticket is "Sky color changes if slot in chest is empty or not"
Your procedure is "Sky color darkening is different between chest inventory and player inventory"
Well, I'm not quite sure what's going on with the sky and UI's, but I suppose it will all get fixed along with this bug.
yes, I'll upload an image (brightness UI) where you can see the difference very clearly between the sky when you're in a chest and the sky when you are in your inventory
A similar thing happens to me: When I open my inventory, the sky darkens after a short delay. When I close it, the sky is still dark, but then brightens after a delay of what appears to be the same length.
I was able to get some screenshots; I'll attach them now.
This happened in the current version (1.5.2), by the way.
yeah, something similar happens to signs and item frames... weird

Fixed in 1.6.1? Can't reproduce it.
confirmed for 1.6.1
uploading a screenshot...

@Jesper the End:
Your screenshot doesn't really follow the tickets description. Hovering over empty/full slots doesn't change the sky color, so I would resolve this ticket as "fixed". Maybe you should take a look at related problems (there are several of them) or open a new ticket for different sky colors when opening inventory or chest GUI.
I guess it's fixed then, do note that this bug doesn't always occur, sometimes it works fine and sometimes it doesn't so once I see it happening again I'll ask to reopen this issue

Is this still a concern in the current Minecraft version 1.6.4 / Launcher version 1.2.5 ? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.
confirmed
Another reproduction method:
Enter creative mode
Note sky colour
Open inventory
Sky colour darkens slightly
Enter survival mode
Note sky colour
Open inventory
Sky colour darkens much more than in creative mode.
When I tried this today, in survival mode the sky seemed to darken twice in very quick succession; so quick it was barely perceptible, even on my slow machine. But the outcome was a much darker background to the inventory UI in survival than in creative. Haven't refound a reliable 'two stage trigger yet' but there is still something funny going on.
Is this still a concern in the current Minecraft version 1.7.2 / Launcher version 1.3.4 ? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.
it seems to be fixed though I might be wrong

Due to someone reporting this is fixed, and due to the changes to this part of them game is this probably
Fixed
If you still experience this issue, please report it here.