The "Best One" is the one you know how to code or can learn easily, and has the inputs/output types, on or off-chip support needed (i.e. xtal/resonator, Schmidt trigger inputs, native PWM outputs etc), and power consumption you require.
Almost all modern design controllers are In Circuit programmed, early PICs and some current ones need an expensive EPROM type programmer to install/change code.
Sometimes, the insane price of a basic stamp with the extra instructions and on board support circuitry will provide everything, but from a performance standpoint, I wouldn't call it "The Best", but in some applications, it is the ticket (advanced end user can make easy software changes, etc).
Look for a chip in a family that has exactly what you need, and you either know the assembly for the family or have a good to pro-level C (or other language) compiler for that controller. Then look at current ratings. Many general purpose use much more current reading 4 inputs, creating 3 PWM outputs, and an LCD simultaneous option which does impact final performance. Sometimes going to a specialized controller (simple 8 pin) will use much less current and perform the function better then a big general purpose with everything 'ignored' except for the function you need. Power consumption/heat play a role, as does clock speed.
I am a PIC fan, but also use AVR and even Basic Stamps on occasion! This is ONLY because I learned PIC assembly first when jumping into the world of microcontrollers.
Others are dedicated to the AVR family, and some prefer a complete processor/RAM/peripheral bus clocked at 10x microcontroller speed to do the same function, as that is what they know (spendy, and low current is out of question, generally)
PIC has a HUGE number of controllers, each with more or fewer features so that your application uses 100% of the device if you choose the correct one. Using a 40+ pin for what could be done by a 8 pin is a waste of time and resources, as the 40 pin packages' circuitry still scans all I/O and options while running the simple program.
For an extreme example of this, would you build a 3Ghz CISC machine (PC, for example), to only write boot code to toggle pins on the parallel port to flash LEDs twice a second? Same can be done for $1 at the controller level,, in addition, the LED's can be bright or dim with PWM output built into that same, low cost item.
I hope the above expands on "Depends on application".
P.S. If I were to do it all over again, I'm sure I'd still be a PIC fan, due to the wide range of devices created so you only get what you need., but can still do most testing/playing on a 16F877, which transfers over to the 'best' specific device with minor modifications.