TblSoftware.softwareVersion is the only field that stores software version numbers. This field is a text field, not a numeric field, and mimics what you see in Add/Remove Programs on the client machine itself. You'll notice that the software version of Office 2010 is not just "14" for instance, but something like "14.0.7015.1000". This is text, not a numeric value.
Using a > or < filter on a text field does not make sense if you are trying to treat the data as numeric values. If you have two text values like the ones below for instance, SQL will consider 2.0 to be "greater than" 10.0. This is because SQL reads text values from left to right. As 2 is greater than 1, 2.0 is considered to be "greater than" 10.0. While this behavior might not be a problem in all situations, you cannot rely on > or < filters added to softwareVersion to give you the results you are looking for.
10.0
2.0
If you want to treat the tblSoftware.softwareVersion values as numeric values, you will need to isolate the relevant version number from the text and convert it to a numeric value. If the "main" version number is the one preceding the first period in the string, you could use CharIndex to isolate it, like so:
Select Top 1000000 tblAssets.AssetID,
tblAssets.AssetName,
tsysAssetTypes.AssetTypename,
tsysAssetTypes.AssetTypeIcon10 As icon,
tblAssets.IPAddress,
tblAssets.Lastseen,
tblAssets.Lasttried,
tblSoftwareUni.softwareName As Software,
tblSoftware.softwareVersion As Version,
Cast(SubString(tblSoftware.softwareVersion, CharIndex('.',
tblSoftware.softwareVersion) - 10, 10) As integer) As MainVersionNumber
From tblAssets
Inner Join tblAssetCustom On tblAssets.AssetID = tblAssetCustom.AssetID
Inner Join tsysAssetTypes On tsysAssetTypes.AssetType = tblAssets.Assettype
Inner Join tblSoftware On tblAssets.AssetID = tblSoftware.AssetID
Inner Join tblSoftwareUni On tblSoftwareUni.SoftID = tblSoftware.softID
Order By MainVersionNumber