If at all there is any difference, I would doubt that you would notice it if you do not run it many, many, many times, or if x and y really do not work so intensively with the processor. I have never seen this interfere as a possible performance issue with Coldfusion with MX 7.
I would recommend using the format that is most readable to you. Adding errors to the code, making them difficult to read, will have a greater impact than differences in performance between the two formats.
Personally, I would prefer to see the NEQ version, as it reads better and is more common in CF.
<cfif x NEQ y>
It says in my head: βIf x is not equal to y ...β Whereas ....
<cfif NOT x EQ y>
reads "if not x equal to y ..." does not make sense in English.
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