Q:

How to program a clean microcontroller?

To be specific, i am interested if there is a way to buy a clean microcontroller (doesn't matter whether it is Atmel or Pic), program it and implement it into your circuit board, without any additional attachments.
PS: Here, additional attachments means something like Arduino, which, apart from microcontroller consists of many other electronics. 
I just want to implement plain (without anything) microcontroller into my circuits.

A:

No, you can't run a microcontroller without anything else in the circuit.  You almost can, but you really need a bypass cap across the power pins of the micro, physically close to the micro.
Other than that, some micros are capable of running without requiring anything else.  Most have a negative-going reset line that needs to be held high for the micro to run.  However, some have a built-in pullup resistor on that line, or can be optionally configured to enable a built-in pullup.  The micro would also need a internal oscillator, but quite a few have that.
One example of a micro that just needs power, ground, and a bypass cap is the PIC 10F200.  The MCLR pin can be configured so that it is a digital input, and the micro always runs when power is applied.  This gives you one input pin, and three pins that can be either input or output, depending on what the firmware does.
There are a number of other PICs that can do this too.  The limiting factor is you need one that can be configured to not do MCLR or with a internal pullup on MCLR.  If you are willing to tie MCLR high, then quite a few more PICs fit your specification.  Some will have multiple power and ground pins, so will require additional bypass caps.  Not all have internal oscillators, but just about all the newer ones do.
If you explain what you want this micro to accomplish, we can probably suggest some models to look at.

A:

In general you will need something to connect a computer to the microcontroller for programming, usually some kind of programmer.
NXP makes a line of ARM microcontrollers that have a built in USB bootloader. If they are blank they automatically enter a bootloader mode that makes them show up as a mass storage device you drop the firmware onto. If you are going to use USB in your circuit this would mean you don't need anything extra. The parts I've used are LPC1343 and LPC1345, others have the same thing, but check before buying them.

