From what I see it's almost always...
Bots/Traffic - Usually some kind of bot wants all your stuff and tries to crawl everything way too fast. Sometimes when the site slows to a crawl they will go away. There can be huge spikes in traffic that don't last long, so they can be easy to miss.
If there happens to be a REALLY BIG resource a hit to that on the PUI can cause trouble as well.
Jobs - The spreadsheet importer can really slow things down. Other background jobs can do the same.
API - Many places have things that hit the API too fast and that'll slow it down.
Big/Complex records - Editing a resource with MANY children and MANY agents and/or subjects can really slow things down. This can be hard to pull out of the logs. A single hit to a monster resource on the PUI could cause trouble as well, loading that
thing is a ton of hits.
Sometimes the spikes end up just being a mystery, but that's rare, and I don't think I've seen that happen more on 4.x any more often than any other version.