I like my iPhone tracking where I've been; my only complaint with Apple is they didn't disclose this useful feature and give me access. But it's not much hacking to get at the data, so I made a map. Red is cell phone towers, blue is wifi nodes. The map looks correct to me; I did a lot of small plane trips in the last year.
My guess is the iPhone is keeping a cache for geolocation. Your iPhone knows where you are by looking up cell phone tower IDs and WiFi MACs; I think the recently discovered file is just a history of those lookups. It's not a very useful tracking file; it doesn't record how often you've been near those points. It does keep timestamps (last seen?) and of course even the cache history is pretty personal data.
On reflection, there's too many points (500+) inside San Francisco, including some in the water, for this to be just cell tower locations from Apple's database. Maybe it is my calculated position? The primary key for the database was named by Apple as MCC+MNC+LAC+CI, which apparently is the "Cell Global Identity". The iPhone only keeps one fix for each; no idea why some are in the water.
Technical details on my secret work blog. The main thing is two tables called CellLocation and WifiLocation which map tower ID or WiFi MAC to a latitude and longitude. The table's big, some 32,000 cell towers and 170,000 wifi nodes. I wrote some quick code to convert the data into GeoJSON and map it with Polymaps. I'd link the zoomable map, but it's personal data and the code isn't optimized.