Those Southern ones will be pretty difficult to beat, although I can't imagine they will ever have sold any of the longer distance ones, at least not as an annual. It takes so long (via Barnham or otherwise!) it would be completely infeasible as any sort of commute, even if only done once or twice a week. So I'm going to stick to journeys that could realistically be commuted on some sort of regular basis.
I suppose it's possible someone clued up might have bought a weekly as a means of relatively cheaply and flexibly 'bashing' particular lines or unit numbers/classes.
In terms of some of the good value PTE fares out there,
Walsden to South Elmsall (WYPTE priced) at £39.10 a week / £1564 a year has to be pretty high up there. 34 miles as the crow flies, 53mi15ch by rail (via Bradford Interchange and Leeds). Assuming you used an annual season as often as a stereotypical office worker (260 weekdays a year less 28 days' holiday = 232 return trips a year) that would average out at £6.74 a day or 6.3p per mile. Such a season would entitle you to take 'detours', via Castleford for example, but I'm just considering the quickest and most likely routes.
Strines to Appley Bridge (GMPTE priced, despite the latter station being just outside Greater Manchester) is nearly as far as the crow flies (32 miles), and costs slightly less at £31.10 a week / £1234 a year. Although in this case the unusually direct route (via Reddish and Atherton is shortest, and fastest most of the time) comes out at just 34mi46ch, so rail distance wise not quite as impressive. Admittedly you could also travel via Golborne Jn to extend the distance by 3mi35ch. Assuming that extension, an annual season works out at £5.32 a day or 7.0p per mile. Notably this season is also valid on the Metrolink around the city centre (in zone 1).
Around London, there are certainly some decent fares priced to avoid Zone 1, but even the plain zonal-priced National Rail-only seasons can be good value when crossing London. For example
Crews Hill to Caterham, a distance of 28 miles as the crow flies, is £52.10 a week / £2084 a year. Distance wise it's 32mi50ch via the quickest route, i.e. using Thameslink between Finsbury Park and East Croydon via London Bridge. That's £8.98 a day or 13.8p per mile. By London standards that's pretty reasonable.