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Jared Robinson gave a simple solution that works on my machine:

Run the following command:

xmodmap -e "pointer = 1 25 3 4 5 6 7 8 9"

To persist this behavior, edit ~/.Xmodmap and add

pointer = 1 25 3 4 5 6 7 8 9

I realise that this is not exactly the answer you want, but you can turn this off in Firefox (e.g. if you don't mind the feature elsewhere, but still want middle click in Firefox to open links in new tabs)

In about:config, set

middlemouse.contentLoadURL false

middlemouse.paste false

Not what you asked, but as this question is linked to from a few places I hope someone finds this answer useful.

I use gnome-tweak-tool for disabling middle button paste in Ubuntu 16.04.

sudo apt install gnome-tweak-tool

Search "tweak tool" in installed apps.
Run it.

Or just type gnome-tweak-tool in a terminal.

Go to "Keyboard and mouse" -> "Middle-click paste"
Turn off.

Thats it.
Tested on Ubuntu 16.04

This currently isn't possible - though, as you have mentioned, there are ways to disable the MOUSE 3 button - or remap it- none of those get at the source of the issue. The X11 Primary Selection.

While this isn't a solution, hopefully this explanation will make it clear WHY. In Ubuntu there are two clipboards at work. One, which everyone is familiar with, the freedesktop.org clipboard (captures Ctrl+C command) The second is a clipboard manager that has been at play since before Ubuntu even existed - X11. The X Server (X11) manages three other clipboards: Primary Selection, Secondary Selection, and Clipboard. When you select text with your pointer it gets copied to a buffer in the XServer, the Primary Selection, and awaits pasting by means of the Mouse 3 button. The other two were designed to be used by other applications in a means to share a common clipboard between applications. In this case the freedesktop.org clipboard manager in Ubuntu already does this for us.

Through the extent of my research I can not find a way to disable the X11 selection manager. There are no compilation flags, applications, or configuration values that can disable this. There are various ways around this on a per application basis (majority of these applications being command line ones) - but nothing on a global scale.

I realize this isn't an ideal solution - but seems to be the truth to the issue. The only relevant solution I could muster is actually a hack, create a script that executes an infinite while loop that just replaces the Primary Selection with a null value.

First install xsel (Tool for manipulation of the X selection) sudo apt-get install xsel

The code is as follows:

while(true)

do

    echo -n | xsel -n -i

    sleep 0.5

done

If you place this in a script and add it to your startup scripts this shouldn't be an issue.

Somehow, I ended up without any xmodmap files on my Ubuntu install, so I had to find a different approach to this problem.

Take a look at the xinput command.

xinput list | grep -i mouse

which lists information about your mouse. It shows my mouse is "Dell Premium USB Optical Mouse" and also that I have "Macintosh mouse button emulation". Armed with that info, I can

xinput get-button-map "Dell Premium USB Optical Mouse"

which gives me a listing that looks like

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18

Here is the useful, required knowledge. My mouse has, theoretically, 18 buttons. Each button's default action has the same name as it's button number. In other words, button 1 does action 1, button 4 does action 4, etc. Action 0 means "off".

The position in the listing shows the function assigned to that button. So if my button map read

1 3 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 

this would mean button 1 (position 1) does action 1 (normal left button), button 2 (position 2) does action 3 (middle button) and button 3 (position 3) does action 2 (right button).

To make a left handed mouse all you would need would be a button map that starts

3 2 1 4 5 .....

Or, in your case, it looks like you want the middle button to do the same thing as button 1 (left button) so your map needs to start

1 1 3 ....

I'd reset my mouse button mappings thus:

xinput set-button-map "Dell Premium USB Optical Mouse" 1 1 3 5 6 6 7 8 9 10 11 12 13 14 15 16 17 18

In your case, you may have a different number of mapped buttons and have some special button map already defined. Likwely, your mouse has a different name, too. First, get your mouse's "name". Then, use the get-button-map operation to find your base button map. finally, use the set-button-map option, modifying button 2 to do action 1.

This is not a permanent change. I added the necessary code to my .bashrc so it executes every time I login or open a terminal.

Hope this helps.

I suggest using one of these, which work mostly well for me:

using xbindkeys:
whenever middle-button is pressed, clear the primary clipboard. At least on my system it is cleared, before the pasting happens.
Details: create xbindkeys-config:

xbindkeys --defaults > $HOME/.xbindkeysrc

Paste the following new hotkey:

"xclip -i /dev/null"    

    b:2``

Reload xbindkeys (e.g. killall xbindkeys;xbindkeys). Done.

using xdotool:
Clear the clipboard on window focus change (should work with most windowmanagers). Details:
Execute the following command:

xdotool search --onlyvisible . behave %@ focus exec xclip -i /dev/null

Note that with this command you can still use the primary clipboard within the same window, or pressing middlemouse onto another window BEFORE focusing it (if you don't have "focus follows mouse", or somthing, activated).

The best way I've found so far is to use EasyStroke, which can globally intercept middle-button click and allow to behave as middle button only in certain apps.

You can add a "group" in EasyStroke to apply this interception in multiple applications at once.
I've set to disable middle click in some of my text editors, IDE and MATLAB only and works as intended.

Reference:
http://ubuntuforums.org/showpost.php?p=11811126&postcount=25

Complete EasyStroke How-To:
http://sourceforge.net/apps/trac/easystroke/wiki/Documentation

This middle mouse button paste behavior is a feature of the X server (and gpm on the text console) and as far as I know at least X.org can't be configured to disable it - all you can do is to change the mapping of the physical mouse buttons as others already suggested.

Chances are good that you can configure your touchpad to avoid unwanted middle clicks, see gpointing-device-settings (not installed by default) or the synaptics manpage if you prefer to use your editor for configuration.

the link below fixed the problem for me.

https://wiki.ubuntu.com/X/Config/Input#Example:_Disabling_middle-mouse_button_paste_on_a_scrollwheel_mouse

the page refered by the above link has a section for how to disable the middle mouse paste on scrollwheel, by executing few commands the user can fetch the mouse buttons mapping and can also change the mapping.
as explained in the page i disabled the the middle button by executing the command:

$ xinput set-button-map 4 1 0 3

I had the same problem a few months ago and I solved it by changing the mouse! But, as you, I was frustrated that simple button mapping problem can't be solved elegantly by a software fix. Fortunately, I had the problem on my job computer, and my employer owns a variety of spare mouse controllers. It was a no cost fix!

I think a proper mouse hardware implementation should not send random middle clicks while scrolling. Recently I found this behaviour to get annoying even while using Windows!

Now that I've fixed the hardware bug with the proper hardware solution (change the mouse) I even started an addiction to "paste on middle-click" behaviour!!

Happy linuxing!

Sincerly,

SW:
Ubuntu 14.04, with Gnome fall back.
HW: I have a laptop and so the middle button is actually the mouse on/in the laptop.
Solution:
Go to Ubuntu SW center and download Unity Tweak Tool.
Start Tweak Tool. Under the Mouse settings it has switch to turn on/off the middle click insert.
Have a lovely day.

I tried the xinput-redirection trick, changing the center mouse "button" (actually a wheel) so it acts just like the left mouse button. It still works as a wheel, and has (apparently) stopped pasting things into random places in the middle of my source code as I scroll past.

In my case the command was

xinput set-button-map "PixArt USB Optical Mouse" 1 1 3 4 5 6 7 8 9 10 11 12 13 14 15 16

but YMMV by mouse model.

I may have a partial answer for you, if you are using a lenovo X... with
touchpoint/touchpad.
There is a "known" bug with the synaptics mouse buttons. If you try a USB mouse
and have no problem, but with the touchpad/touchpoint mouse (build into the keyboard) you do have random responses that can delete swaths of text as you type, then this may be the bug I'm talking about.

https://bugs.launchpad.net/ubuntu/+source/linux/+bug/1506817

If this fits your situation, then add your name to the list of people who have identified this bug, at that bug report. Maybe if there are many more of us reporting this, it would get fixed.

Here's the simplest solution I've found to keep middle click functional without it pasting things.

First install sxhkd and xsel.

Then configure ./.config/.sxhkd/sxhkdrc like so

~button2

    echo -n | xsel -n -i

~control + c

    echo -n | xsel -n -i

~control + x

    echo -n | xsel -n -i

And that's basically it.

Now start sxhkd (or configure it to launch on startup). Now, middle mouse will no longer paste anything but will otherwise function like normal. (As long as you use only ctrl+c and ctrl+x to copy things that is, if you copy things with the mouse it can paste once before it returns to normal.)

It's more than a gnome feature, i think it works almost everywhere, it works in the console too, and I think it worked even in my "Linux from Scratch".

So it's really a basic feature perhaps even somewhere in the kernel.

BTW: It's really useful, and it's not the regular paste like Ctrl + V, everything that is marked with the cursor goes in a second storage and with middleclick can paste, what you marked last.

Using what I learned in the posts above, this bash one-liner works perfectly for me...

mouse_id=$(xinput list | grep 'Mouse' | awk '{print $9}' | sed 's/[^0-9]//g') && xinput set-button-map "$mouse_id" 1 0 3

You might want to try emulating a two button mouse. With a two button mouse you paste by clicking both mouse buttons at the same time (rather then the scroll wheel).

Install gpointing-device-settings:

sudo aptitude install gpointing-device-settings

http://live.gnome.org/GPointingDeviceSettings

Alternately, if you do not wish to install gpointing-device-settings , and you are not bothered by command line options, see https://wiki.ubuntu.com/X/Config/Input On this wiki page there are several command line / configuration options, choose the one you prefer.

That's a good question, which i don't have an answer for (yet).
A quick and dirty workaround is to remap it NOT to 0, but to 1.
This way, it turns middle-"click" to left click, and does not affect your scroller...
It is so far the best I can think of.

Note:This information came from Ubuntu Forums, not my own noggin! :)