Opto-coupler (CTR) and PWM/Relays
As i increase the resistance of photo diode of opto-coupler (4N35) the resistance between collector and emitter increases too.


Nope.  As you increase the current going through the photodiode, the current passed through the transistor increases.  Resistance is a linear phenomenon, transistors and diodes are nonlinear.


  How the resistance between collector and emitter of opto-coupler affects the transistor in a opto isolator circuit which is gonna run a relay or mosfet?


The diode is an LED; it emits light.  The phototransistor responds to light as if it were current on the transistor base.  The "resistance" you are talking about is the effect where more current is passed in the transistor as more light is emitted from the LED.  This current can be used to switch following electronics, such as a transistor that powers a relay.


  What does current transfer ratio % means? for example 4N35 CTR is 100% while 4N28 is 10%. is lower better? [source]


Output current = (CTR) * (input current).  More is better.


  How fast can an opto-coupler turn on/off, is it suitable for PWM?


Relatively slowly.  It's in the data sheet.  Whether it's suitable for PWM depends on the speed of your PWM.


  What's the difference between this two schematics, why in first one the base pin of opto-coupler is also used?


It looks like the top schematic is supposed to be linear, with Vout going down as Vin goes up.  The bottom schematic is just supposed to turn the relay on and off.