Here is something I threw together quickly. It has parameter to determine whether or not to do case-sensitive comparison of values and keys. Throw these two functions (StructEquals(), ArrayEquals()) in some kind of utilities CFC.
Limitation: Does not work for structs/arrays containing queries or objects.
<cffunction name="StructEquals" access="public" returntype="boolean" output="false"
            hint="Returns whether two structures are equal, going deep.">
  <cfargument name="stc1" type="struct" required="true" hint="First struct to be compared." />
  <cfargument name="stc2" type="struct" required="true" hint="Second struct to be compared." />
  <cfargument name="blnCaseSensitive" type="boolean" required="false" default="false" hint="Whether or not values are compared case-sensitive." />
  <cfargument name="blnCaseSensitiveKeys" type="boolean" required="false" default="false" hint="Whether or not structure keys are compared case-sensitive." />
  <cfscript>
    if(StructCount(stc1) != StructCount(stc2))
      return false;
    var arrKeys1 = StructKeyArray(stc1);
    var arrKeys2 = StructKeyArray(stc2);
    ArraySort(arrKeys1, 'text');
    ArraySort(arrKeys2, 'text');
    if(!ArrayEquals(arrKeys1, arrKeys2, blnCaseSensitiveKeys, blnCaseSensitiveKeys))
      return false;
    for(var i = 1; i <= ArrayLen(arrKeys1); i++) {
      var strKey = arrKeys1[i];
      if(IsStruct(stc1[strKey])) {
        if(!IsStruct(stc2[strKey]))
          return false;
        if(!StructEquals(stc1[strKey], stc2[strKey], blnCaseSensitive, blnCaseSensitiveKeys))
          return false;
      }
      else if(IsArray(stc1[strKey])) {
        if(!IsArray(stc2[strKey]))
          return false;
        if(!ArrayEquals(stc1[strKey], stc2[strKey], blnCaseSensitive, blnCaseSensitiveKeys))
          return false;
      }
      else if(IsSimpleValue(stc1[strKey]) && IsSimpleValue(stc2[strKey])) {
        if(blnCaseSensitive) {
          if(Compare(stc1[strKey], stc2[strKey]) != 0)
            return false;
        }
        else {
          if(CompareNoCase(stc1[strKey], stc2[strKey]) != 0)
            return false;
        }
      }
      else {
        throw("Can only compare structures, arrays, and simple values. No queries or complex objects.");
      }
    }
    return true;
  </cfscript>
</cffunction>
<cffunction name="ArrayEquals" access="public" returntype="boolean" output="false"
            hint="Returns whether two arrays are equal, including deep comparison if the arrays contain structures or sub-arrays.">
  <cfargument name="arr1" type="array" required="true" hint="First struct to be compared." />
  <cfargument name="arr2" type="array" required="true" hint="Second struct to be compared." />
  <cfargument name="blnCaseSensitive" type="boolean" required="false" default="false" hint="Whether or not values are compared case-sensitive." />
  <cfargument name="blnCaseSensitiveKeys" type="boolean" required="false" default="false" hint="Whether or not structure keys are compared case-sensitive, if array contains structures." />
  <cfscript>
    if(ArrayLen(arr1) != ArrayLen(arr2))
      return false;
    for(var i = 1; i <= ArrayLen(arr1); i++) {
      if(IsStruct(arr1[i])) {
        if(!IsStruct(arr2[i]))
          return false;
        if(!StructEquals(arr1[i], arr2[i], blnCaseSensitive, blnCaseSensitiveKeys))
          return false;
      }
      else if(IsArray(arr1[i])) {
        if(!IsArray(arr2[i]))
          return false;
        if(!ArrayEquals(arr1[i], arr2[i], blnCaseSensitive, blnCaseSensitiveKeys))
          return false;
      }
      else if(IsSimpleValue(arr1[i]) && IsSimpleValue(arr2[i])) {
        if(blnCaseSensitive) {
          if(Compare(arr1[i], arr2[i]) != 0)
            return false;
        }
        else {
          if(CompareNoCase(arr1[i], arr2[i]) != 0)
            return false;
        }
      }
      else {
        throw("Can only compare structures, arrays, and simple values. No queries or complex objects.");
      }
    }
    return true;
  </cfscript>
</cffunction>
Unit Tests for anyone interested:
public void function test_StructEquals() {
  AssertTrue(utils.StructEquals({}, StructNew()));
  AssertTrue(utils.StructEquals({}, StructNew(), true, true));
  AssertFalse(utils.StructEquals({}, {"a": "b", "c": "d"}));
  AssertTrue(utils.StructEquals({"a": "b", "c": "d"}, {"C": "D", "A": "B"}));
  AssertFalse(utils.StructEquals({"a": "b", "c": "d"}, {"C": "D", "A": "B"}, true, false));
  AssertFalse(utils.StructEquals({"a": "b", "c": "d"}, {"C": "D", "A": "B"}, false, true));
  AssertTrue(utils.StructEquals({"a": "b", "c": "d"}, {"C": "d", "A": "b"}));
  AssertTrue(utils.StructEquals({"a": "b", "c": "d"}, {"C": "d", "A": "b"}, true, false));
  AssertFalse(utils.StructEquals({"a": "b", "c": "d"}, {"C": "d", "A": "b"}, false, true));
  AssertTrue(utils.StructEquals({"a": "b", "c": "d"}, {"c": "D", "a": "B"}));
  AssertFalse(utils.StructEquals({"a": "b", "c": "d"}, {"c": "D", "a": "B"}, true, false));
  AssertTrue(utils.StructEquals({"a": "b", "c": "d"}, {"c": "D", "a": "B"}, false, true));
  var stc1 = {
    "test": {
      "hello": "world",
      "goodbye": "space",
      "somearr": [
        { "a": 1, "b": 2 },
        "WORD",
        [
          { "x": 97, "y": 98, "z": 99 },
          { "i": 50, "j": 51, "k": 52 }
        ]
      ]
    }
  };
  var stc2 = {
    "test": {
      "goodbye": "space",
      "hello": "world",
      "somearr": [
        { "a": 1, "b": 2 },
        "WORD",
        [
          { "z": 99, "x": 97, "y": 98 },
          { "i": 50, "k": 52, "j": 51 }
        ]
      ]
    }
  };
  AssertTrue(utils.StructEquals(stc1, stc2, true, true));
  stc2.test.somearr[2] = "WOrD";
  AssertTrue(utils.StructEquals(stc1, stc2));
  AssertTrue(utils.StructEquals(stc1, stc2, false, true));
  AssertFalse(utils.StructEquals(stc1, stc2, true, false));
  stc2.test.somearr[3][1] = { "z": 99, "X": 97, "y": 98 };
  AssertTrue(utils.StructEquals(stc1, stc2));
  AssertFalse(utils.StructEquals(stc1, stc2, false, true));
  AssertFalse(utils.StructEquals(stc1, stc2, true, false));
  stc2.test.somearr[2] = "WORD";
  AssertTrue(utils.StructEquals(stc1, stc2));
  AssertFalse(utils.StructEquals(stc1, stc2, false, true));
  AssertTrue(utils.StructEquals(stc1, stc2, true, false));
}
public void function test_ArrayEquals() {
  AssertTrue(utils.ArrayEquals([], ArrayNew(1)));
  AssertTrue(utils.ArrayEquals([], ArrayNew(1), true, true));
  AssertFalse(utils.ArrayEquals([], [1, 2, 3]));
  AssertTrue(utils.ArrayEquals(['a', 'b', 'c'], ['A', 'B', 'C']));
  AssertFalse(utils.ArrayEquals(['a', 'b', 'c'], ['A', 'B', 'C'], true, false));
  AssertTrue(utils.ArrayEquals(['a', 'b', 'c'], ['A', 'B', 'C'], false, true));
  AssertFalse(utils.ArrayEquals(['a', 'b', 'c'], ['a', 'c', 'b']));
  AssertTrue(utils.ArrayEquals([1, 2, 3], [1, 2, 3]));
  AssertFalse(utils.ArrayEquals([1, 2, 3], [1, 3, 2]));
}