Which USB slot is 2.0 or 3.0? How do I know?

According to the Wikipedia page on USB:

Colors

Ports and connectors are often color coded to distinguish different functions. These colors are not part of the USB specification and can vary between manufacturers.

- USB 1.x               White
- USB 2.0               Black, sometimes white
- USB 3.0               Blue
- Sleep-and-charge      Yellow or red

As an additional identifier if you look at the USB 3.0 Wikipedia page:

First introduced in 2008, USB 3.0 adds a new transfer mode called "SuperSpeed," (distinguishable from USB 2.0 by either the blue colour of the port or the initials SS)

as well as this:

Since USB 2.0 and USB 3.0 ports may coexist on the same machine and they look similar, the Standard-A USB 3.0 connector has a blue insert (Pantone 300C color). The same color-coding applies to the USB 3.0 Standard-A plug.

As to the cabling (and sometimes the ports themselves, notice the "SS" on the cabling, it stands for Super Speed which is the naming for 3.0 USB.

                                       

From the command line?

lsusb

You can also use lsusb to identify which ports are rated as USB 2 vs. 3 like so:

$ sudo lsusb -v | grep -iE "Bus|^Device Desc|bcdusb"
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Device Descriptor:
  bcdUSB               2.00
Bus 002 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Device Descriptor:
  bcdUSB               2.00
Bus 003 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Device Descriptor:
  bcdUSB               1.10
...
...
Bus 010 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub
Device Descriptor:
  bcdUSB               3.00

NOTE: each device that has a 1.10 is one of the typically yellow USB ports that are always powered on.

lspci

You can also do something similar with lspci.

$ sudo lspci | grep USB
00:1a.0 USB controller: Intel Corporation 82801JI (ICH10 Family) USB UHCI Controller #4
00:1a.1 USB controller: Intel Corporation 82801JI (ICH10 Family) USB UHCI Controller #5
00:1a.2 USB controller: Intel Corporation 82801JI (ICH10 Family) USB UHCI Controller #6
00:1a.7 USB controller: Intel Corporation 82801JI (ICH10 Family) USB2 EHCI Controller #2
00:1d.0 USB controller: Intel Corporation 82801JI (ICH10 Family) USB UHCI Controller #1
00:1d.1 USB controller: Intel Corporation 82801JI (ICH10 Family) USB UHCI Controller #2
00:1d.2 USB controller: Intel Corporation 82801JI (ICH10 Family) USB UHCI Controller #3
00:1d.7 USB controller: Intel Corporation 82801JI (ICH10 Family) USB2 EHCI Controller #1
02:00.0 USB controller: NEC Corporation uPD720200 USB 3.0 Host Controller (rev 03)

Again in the output, ports marked as USB are the always powered on type (aka. Sleep-and-charge ports), while USB2 and USB 3.0 are marked accordingly.

There are a number of questions.

To the first bunch of questions, your computer's chipset doesn't support USB3. You could add a plugin card that provides USB3 ports - in that case, only the ports provided on the card are USB3, while your existing ports remain USB2. See http://www.newegg.com/Product/Product.aspx?Item=N82E16815166026 (for a laptop) or http://www.newegg.com/Product/Product.aspx?Item=N82E16839314014 (for a desktop computer) as example.

As to your last question, which ports are USB1 and which are USB2: All ports are both.

The USB1 (UHCI) controllers are called "companion controllers" in the USB standard. By default, all ports are routed there (for compatibility with operating systems without EHCI driver), but in a way that the USB2 (EHCI) controller can take over if the USB driver detects a USB2 device.

This means that when you attach a USB1 device (eg. a keyboard) and a USB2 device (eg. a thumb drive) to the same port, they will appear at different locations in the lsusb output. The USB2 device will end up at an EHCI controller while the USB1 device ends up at an UHCI controller. There is no 1:1 relation between physical ports and controllers.

You can determine the mode a device is operating under in lsusb in the device line itself: Port 2: Dev 2, If 0, Class=HID, Driver=usbhid, 12M, 12M means 12MBit/s = USB1, 480M = 480MBit/s = USB2, 5000M = 5000MBit/s = USB3.

It's different with USB3 since it comes with a different port design - 9 lines in two rows instead of 4 in one, and many devices come with dedicated USB3 ports and some additional USB2 ports (since they're cheaper).

To easily identify them, the USB3 standard mandates that USB3 ports must have a blue insert.