Prejudice can be defined as a judgement or opinion that one has to a person, thing or situation which is not based on actual experience or rational thought. The term is usually used to define a preconceived value or appreciation that one attaches to other people with whom one has dealings with, whether for a brief moment or a lengthy period of time. As mentioned in the question, racism is an example of prejudice.
In the play, prejudice also rears its ugly head in the association between Shylock and his servant, Launcelot. It is obvious that Shylock ill-treats Launcelot and does not give him his due. This is because Shylock sees him as below his status and thus deems him inferior. It is impossible for him to perceive Launcelot as an equal in human terms and he, therefore, maintains a supercilious approach towards him. Shylock's abuse clearly upsets Launcelot and he decides to leave his service and work for Bassanio, who, he believes, will treat him better.
Launcelot distinctly states his dissatisfaction with Shylock's treatment of him when he speaks to his father, Gobbo in scene 2 of Act 2 (lines 111 to 117):
...My master's a very Jew: give
him a present! give him a halter: I am famished in
his service; you may tell every finger I have with
my ribs. Father, I am glad you are come: give me
your present to one Master Bassanio, who, indeed,
gives rare new liveries: if I serve not him, I
will run as far as God has any ground...
Launcelot wants to get as far away from Shylock as possible and states that if he should not be appointed by Bassanio, would run as far as he possibly can to be rid of Shylock.
In her conversations with Nerissa, Portia also displays a somewhat prejudicial attitude towards her suitors. She makes a number of derogatory remarks about them without really knowing much about their background or who they really are. She is quite judgmental in her approach.
This may be borne from her displeasure of not being able to have the freedom to choose a partner and is an expression of her irritation with the limitations set by her father's will, or it may be a reflection of a natural inclination to judge by what she sees. She does not have much choice in the matter anyway, and may be forgiven her sentiments in the circumstances.
Her preconceived notions are best illustrated when she says, in Act 1, scene 2, (lines 41 - 43), the following about the prince of Morocco whom she has not seen yet:
...if he have the condition
of a saint and the complexion of a devil, I had
rather he should shrive me than wive me...
Her statement suggests a racist prejudice, for the suggestion is that if the prince were black, she would prefer him hearing her confession (as a priest would) than be his wife.
She does, however, display a favourable prejudice towards Bassanio, whom she also does not really know, as she states in Act 1, scene 2:
PORTIA
Yes, yes, it was Bassanio; as I think, he was so called.
NERISSA
True, madam: he, of all the men that ever my foolish
eyes looked upon, was the best deserving a fair lady.
PORTIA
I remember him well, and I remember him worthy of
thy praise.
One can also deem Antonio's attitude towards Shylock's moneylending practice as a form of economic prejudice. Criticising the Jew for lending out money at interest, implies that Antonio wishes to limit Shylock's source of income. Moneylending is his business and denying him the right to lend out money for profit without truly understanding the practice, is harmful to the Jew. Shylock mentions Antonio's disdain in this regard in scene 3 of Act 1 (lines 49 - 52):
...he rails,
Even there where merchants most do congregate,
On me, my bargains and my well-won thrift,
Which he calls interest.