when Shift clicking into containers, from the hot bar to inventory ,and viceversa all are not working. Also trying to drag an item and drop it over another in order to replace it in creative and survival is not working.
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This bug is crippling to my game play as a heavy user of shift click. 😞

What do you mean with all are not working
?
Does is not work at all for you or only sometimes ?

Simplifying this ticket to the most prominent of the multiple bugs posted here. It is much easier for us to deal with bug reports when they contain only one bug. Feel free to create new ticket(s) with additional bugs.

Please get this fixed! I started playing mc 1.5 and I almost straight away noticed the lack of shift-click.
Edit: I discovered that any interaction (except moving) when holding shift will often cancel the shift
Please provide additional information, so we can better help with your problem:
Was this a single player or multi-player/LAN game?
Was the issue corrected after logging out and back in?
Was the issue corrected after closing the program and restarting?
Have you been able to reproduce this?
You may also want to review the guidelines for writing helpful bug reports.

I have now discovered the reason this isn't working! The problem is that any mouse interaction cancels any keyboard input!
Edit: It appears to work fine on Toshiba, but not on Lenovo
I can't get the new inventory management system (double-clicking, shift+drag, shift+double-click) to work at all. I know the system has changed since 1.4.7, but I don't think it's supposed to be the way it's acting on my system now.
Right-clicking still halves a stack, but none of the double-clicking options seem to be working. Shift+drag appears to work sporadically, but very, very slowly, having to pause for several seconds over each crafting box (often wiggling the mouse back-and-forth) to get it to drop items. When it does work, the item count doesn't always update correctly.
These problems occur in both single-player and my own multi-player server, and didn't exist for me in 1.4.7. I have not had time to check it on my other system.
Attached a crash report above.
Are you playing on a CraftBukkit server? I have similar problems (I'm not able to craft anything). I think this is a CraftBukkit server issue. Not sure. See https://bukkit.atlassian.net/browse/BUKKIT-3789
Updated with screenshots and a short description of some of the inventory management problems I've had in 1.5.
Edit: Upgrading graphics card drivers from Catalyst 12.4 to 13.1 had no effect on this problem.

@MrHeat: Nope, using vanilla, started in single and later opened to LAN, before opening shift would get cancelled by the mouse and after opening it would still happen for me, but my friend who joined and was using a Toshiba was working fine
Everything works fine on my other system (a laptop), with no problems whatsoever. I tested it out in both single-player and multi-player. I'm attaching a crash report from this system as well (crash-2013-03-18_14.25.33-client.txt) for comparison purposes.
Please try following this Tutorial on how to update LWJGL and see if that helps.
Tails: No such luck on updating the library. I also updated both versions of Java (32 and 64 bit) to the latest releases today with no changes.

Using lwjgl 2.8.4 the bug does not exist! Turns out it is a bug with 2.8.5
Problem still exists with LWJGL 2.8.4 for me.
So how was this resolved? I'm having the same issue.
If you play in windowed mode, the mouse de-focuses the window. This causes the keyboard to be "interrupted". If you are playing windowed mode, try playing fullscreen. If the problem doesn't persist, then this should be labeled "resolved".
Yes, I do normally play windowed mode. Unfortunately, switching to fullscreen doesn't fix the issue.
Deleting my .minecraft folder on the other hand has fixed the problem. Hooray!