Should the relationship between an employee and his boss reflect on the employee's appraisal?

No.  the relationship between an employee and his boss should be a prefessional relationship.  In a professional relationship, there is no room for like/dislaike and therefor the relationship should have no impact on appriaisal.

Type of Relation would determine the suitable Answer:

Professional Relation:

a) supervisor must determine appraisal unbaised based on accomplishment of KRA's and KPI's.

b) Supervisor must clearly represent score to the employee based on the facts that would emerge from Percent earned out of achiving KPI

c) Supervisor's conduct must remain to fair to the employee and to the organization too.

d) If some of the above is maintained the relation would always be cordial between employee and Supervisor.

If the relation is Personal in most of the cases the appraisal, its process is deemed to be unfair. It might be fair in very few little percent if the process is conducted in unbaised manner. The biggest tragedy that emerges out of unbaised maaner remains, opportunity lost to learn, Opportunity to grow with the organization etc.

It shouldn't, and if it does you know you're dealing with an unprofessional boss.

In reality, yes. There is an influence even though it is against the organization's policy as the professionalism of any type of work must segregate emotions with business. From the manager view, there should an expectation of how his/her staff are performing their duties no matter if he/she likes their personalities or not. The relationship line can become emotionally charged.

I believe that whatever the relationship between a manager and a subordinate, the appraisal must be impartial and based on the KPI's outlined. Performance is the only criteria, and any relationship between the two, personal or otherwise cannot exist in the equation. 

If a manager is influenced by relationships, then the worker's performance appraisal will be compromised, one way or the other. Personal issues should not and cannot be a factor in performance appraisal.

HR must create this both enact and espouse this environment, as it will create unhealthy situations for the organization. 

It should not because there should never be a "relationship" between the employee and his/her boss.  If you mean their work relationship only and this includes things like communication, attitude, and general affect...then YES it is part of the evaluation.  If someone is grumpy at work or constantly a mean person, I don't care how good they are at their job, there is a social expectation to all jobs.  Being able to socialize with coworkers without creating a nusience is part of being a good employee

Yes, it's very apparent and visible too, practically.

As an Coorporate Employee no is the answer.

But as an practical man yes is the answer.

Manager / employee relationship should not affect the employee's appraisal if the manager is a professional, but this is not always the case. The fact is personal feelings often interferes with sound judgement.

Yes....Appriasal depends upon like & dislike of the boss. Even in some cases emlpoyee & Boss realtions are good but if top management dont enforce it, then also emloyee can not get good appraisal.

Yes the relationship between Boss and Employee can cause element of biasness during appraisals, if the appraisal is two way e.g Boss gives feedback of employee and employee give feedback of boss. They both can create Win-Win situation for one another. 

But if the company has strong standards of their Performance Management System (PMS) and is Goal Oriented then relationship doesn't matter. Obviously there will be a chain of command where someone will be appraising the entire department including Boss and his team !!!