Select 2 computers, then run this report. It will show you if an application only exists on one of them, or if each of them has a different version.

Application Comparison with Version.sql

-- https://gist.github.com/Colby-PDQ/133fdcc7596d8908d6f43a195b9e02f2

SELECT
	  Computers.Name AS "Computer Name"
	, Applications.Name AS "Application Name"
	, Applications.Version AS "Application Version"
FROM
	(
		SELECT
			  Applications.ApplicationId
			, COUNT(Applications.Name || Applications.Version) AS "ApplicationCount"
		FROM
			Applications
		INNER JOIN
			Computers USING (ComputerId)
		WHERE
			<ComputerFilter>
		GROUP BY
			Applications.Name || Applications.Version
	) ApplicationCounts
INNER JOIN
	Applications USING (ApplicationId)
INNER JOIN
	Computers USING (ComputerId)
WHERE
		<ComputerFilter>
	AND
		ApplicationCounts.ApplicationCount = 1
ORDER BY
	Applications.Name COLLATE NOCASE

Application Comparison with Version.xml

<?xml version="1.0" encoding="utf-8"?>
<AdminArsenal.Export Code="PDQInventory" Name="PDQ Inventory" Version="16.5.0.0" MinimumVersion="3.1">
  <Report>
    <ReportDefinition name="Definition">
      <Sql>-- https://gist.github.com/Colby-PDQ/133fdcc7596d8908d6f43a195b9e02f2

SELECT
	  Computers.Name AS "Computer Name"
	, Applications.Name AS "Application Name"
	, Applications.Version AS "Application Version"
FROM
	(
		SELECT
			  Applications.ApplicationId
			, COUNT(Applications.Name || Applications.Version) AS "ApplicationCount"
		FROM
			Applications
		INNER JOIN
			Computers USING (ComputerId)
		WHERE
			&lt;ComputerFilter&gt;
		GROUP BY
			Applications.Name || Applications.Version
	) ApplicationCounts
INNER JOIN
	Applications USING (ApplicationId)
INNER JOIN
	Computers USING (ComputerId)
WHERE
		&lt;ComputerFilter&gt;
	AND
		ApplicationCounts.ApplicationCount = 1
ORDER BY
	Applications.Name COLLATE NOCASE</Sql>
      <ReportDefinitionTypeName>SqlReportDefinition</ReportDefinitionTypeName>
    </ReportDefinition>
    <Created>2018-10-24T12:44:55.0000000-06:00</Created>
    <Description>Select 2 computers, then run this report. It will show you if an application only exists on one of them, or if each of them has a different version.</Description>
    <IsNew value="false" />
    <Modified>2018-10-24T13:43:50.0000000-06:00</Modified>
    <Name>Application Comparison with Version</Name>
    <Path>Reports\Application Comparison with Version</Path>
    <ReportFolderId value="1" />
    <TypeName>SqlReport</TypeName>
    <ReportType>SqlReport</ReportType>
  </Report>
</AdminArsenal.Export>

Revision 2: Simplified the logic and cleaned up the output. Having separate columns looks a LOT nicer than tacking the version on with "---" :)

Revision 3: Added a link to this gist.