There are many different SPI programmers on the market right now and almost any microcontroller-based board can be used as one, but this time I will speak about one of the cheapest programmers to date - CH341A-based.
They are sold from various chinese suppliers for about 4 euro and are capable of flashing with both SPI and I2C chips, working as USB-TTL adapter and USB-I2C bridge.
In this guide I will only cover the SPI part of functionality because this is what you need to flash modified or restore original firmware on all modern PCs.

0. Get yourself a CH341A-based programmer. They are various in PCB designs and features, but all of them can flash SPI chips, so buy any model suitable for your needs. I've bought this one (ebay.de).
1. Download the software. Windows-version is attached to this post, version for Linux is here. Required drivers will be installed automatically (if not, just google for them).
2. Connect the programmer to your flash chip. If your chip is in DIP-case (i.e. you have desktop motherboard with socketed BIOS chip), just gently plug it out, insert into programmer's ZIF-socket and press the lever to fix it in position. If your chip is in SOIC-case, you can use the supplied converter board, SOIC test clip, another ZIF-socket or just solder a tiny wires onto chip's pins. You can also try in-system programming (i.e. programming the chip without desoldering it) but it can easily fail because the programmer needs to provide power for the half of the motherboard that way, and results of such tries are not predictable. Sometimes it works, sometimes it's not, it's for you to decide.
3. Connect the programmer to USB port and run the software. Select 25 SPI Flash as Type and press Detect button, your chip should be detected.

4. Press Read and wait for the operation to complete. Press Save and save your chip contents as backup somewhere.

5. Press Open and select the image you want to flash. Press Erase to erase chip contents, it's very fast on most chips. Press Program and wait for the operation to complete.

6. Press Verify and wait for the operation to complete. If the chip is OK, verification will be successful, if not - check your connections, try to erase the chip first and repeat the whole process.

7. Disconnect the programmer from USB, return the SPI flash chip to it's original place and try to boot the PC. If your image was OK, the system should work now.

EDIT by Fernando: Insecure eBay link replaced by a secure one

Hello what you think about Gzut dream pro 2 i have it but i was unsucsess to flash empty chip on asus maximus hero VII
Its program correct chip but its not boot up UFB flashes it also but pc not post possible its not like type of my chip.
I ask is anyone got empty chps flashing work on Z97 mobos.

It's OK too, even faster, but not as cheap as CH341A-based ones.
I have also seen that Z97 boards have problems working with non-factory flash chips, but I don't know the reason of it. All of modern SPI chips has a page of write-once memory to write some vendor data, which can then be read by a special SPI command, but I don't have such system to test and find out, so I simply don't know.

Yes, but you will require an external power supply to power chip's 3.3V voltage rail and a SOIC clip to connect to it.

3.3V is definitely supplied by USB interface, but it's only about 100 mA current possible for cheap programmers because of cheap components. It's more then enough for SPI chip along, but can be not enough to power the half of a board during ISP.
If the system is powered up, you don't need any other power supply - system's suply is enough.
You need SOIC 8 pin 1,27mm pitch test clip, like this one.

Yes, they are all compatible and based on the same reference desing.
The socket is for 2 8-pin DIP-300 packaged chips, one part is for 24x series (I2C interface), another is for 25x series (SPI interface).
Some programmers also have a pin header with SPI signals (Power, Ground, CS, CLK, MOSI and MISO), so you can connect it to 16-pin chips using jumper wires, but the socked is for 8-pin ones.

is it possible to flash chip while system is turned on(windows running???)?

i'm trying to flash bios on my chip Winbond w25q64fv but once i connect cable to chip i get device status: not connected (chip soldered to motherboard)

Could it be because of not enough power power from programmer? or do you think it can be anything else? (i tried on win 8.1 64bit and win 7 32bit)
you think i'll run into any trouble because the chip is w25q64FV and the software supports w25q64BV

I was afraid of that too. Now you need to desolder the chip, there is nothing you can do without desoldering.

The main problem by ISP is not the main power, but data lines power, which is normally not enough if driven from cheap non-ISP-ready programmer. You can try to desolder just the power line and use the power from the SOIC clip, but it will be much better to desolder the whole chip, which can be done using a hot air station or just a normal soldering iron combined with solder wick.