I have several favorite lines
SE London: The North Kent line, sometimes known as the Woolwich line, the main line for the Dartford/Medway routes, I grew up along this line in the 90s and when the slam door trains were being phased out, the Charing Cross to Gillingham service was the last service to still use them, I loved travelling from Gillingham through the Medway towns, to Gravesend, passing the Kentish/London suburbs at speed, I find it an underrated line myself.
South London: I like the Oxted lines, especially going into Victoria, it reminds me of alot of suburban lines north of the river where the tube provides the "stopping" service while The NR service provides the "fast/express" service, I especially enjoy the non stop run between
East Croydon and Clapham Junction, and the beautiful Wealden countryside too.
SW London: The Waterloo to Windsor/Reading line, similar in nature to the Woolwich line really,
The London to Aylesbury line is my absolute favourite line north of the Thames, the way it zooms all the way to Harrow in ten minutes from Marylebone, then the next thing you know its the countryside.
Outside London, I like the York to Leeds line, I spent some time in Knaresborough a few years ago and I used this line alot, I loved the bleakness of the route.