In my opinion, if you've got a patch, that you've documented pretty well (what it does, what it touches/changes), it would only be a smidge more work to actually runn diffs on standard-release (your pre-patch versions) versions against the previous "standard" release, so you can tell what got changed, and if it affects your patch (assuming they don't give detailed changelogs with new releases). If you actually kept track of what files your patches affect (should), you could even automate the new version diffs to check your list of files affected by your custom patch, and alert you of possible conflicts, or just auto-apply if no conflicts are found.
I'm not sure there is a "clean"/"easy" way to do what you want :/ At least with rolling your own patches, if they aren't affected by changes in new standard releases/trunk, they should apply in milliseconds.
If you're looking for a visual diff/compare utility, check out Files Comparer. It may not be the best or fanciest, but it's free.