There are a few possibilities:
1. Verify you have not been infected by a virus. See my preferred method from safe mode as described at the start of my post
HERE (even though you are not getting BSODs the virus scan is the same).
2. Your mouse drivers may have been updated. Now the fact you get this with a USB mouse and the touch pad makes this
relatively unlikely simply because they probably use different drivers and so windows update is not likely to have updated them both to problem drivers at the same time. But still you can go to control panel > device manager and locate your mouse in the list, open properties > driver tab and see the driver date and see if the rollback driver option is available. If the driver is recent and the rollback option is available then try rolling it back to an older driver to see if that helps.
3. Most likely your processor is busy and just isn't "getting around" to processing your mouse actions. This is the most likely situation but the hardest to deal with. This can be caused by a virus (thus #1 above) but it can really be caused by any intense software actions such as your anti-virus software, toolbars, etc getting bogged down.
I had a situation where my mouse would seem to stall about every 15 minutes ... turned out in my case it was updating the DNS at that time and because I had a huge hosts file it would take a couple minutes; if you don't know what a hosts file is then this is probably not your issue but it is an example.
One thing you can do is install
Process Explorer and then adjust your windows so you can see it even while you are working in another window, then when you notice the mouse failing to respond you look over at Process Explorer and see what program is taking all your CPU. If it turns out to be a SVCHOST then a little more research is needed to find out exactly what service, but if it is a program exe then you know that is the most likely cause.
It is quite possible the issue bogging down your computer might be updates: Windows Updates, Google Updates, Flash updates, java updates, Anti-Virus updates: because you have a laptop it is likely turned off a good portion of the day which means when you turn it on everything tries to update when you finally turn it on. Personally I disable all of this automatic updating except my anti-virus but if you do that then you need to take the responsibility to run it manually; a happy medium might be to set them to notify you of updates but not to download and install until you manually allow it.
It is also a good idea to uninstall unused toolbars and remove programs from startup that aren't needed.
