For London, the South, East Anglia and the Midlands, my "Top 5" ranking would have to be:
1. Chiltern (I rarely ever find serious punctuality issues, their staff seem knowledgable, and they have a very good reputation of decent customer service & onboard experience, bar late evenings at Marylebone; one sticking point is 67 reliability)
2. FGW (I often find punctuality misses out, but the rest seems to be quite good - HSTs, premium options, social media, station managers, you name it - and they even try to make Pacer journeys feel a little better; many overall issues are down to a vocal set of daft passengers)
3. GA (yes, really - my journeys & staff encountered have generally been OK, with a good reason given if something's gone wrong or the stock isn't satisfactory; also, their 360s and refurbished 156s are very acceptable on most applicable workings)
4. SWT (when I've commuted with them, I have rarely seen serious issues which they haven't handled as best as possible, given the intense services, and the guards & station staff are usually friendly and happy to help; their NR Alliance is also an excellent move)
5. Joint between c2c & London Overground (both of which are busy & largely punctual operators, who seem to know what they're doing and take pride in keeping things clean & tidy as far as they can; however, some London Overground revenue staff are somewhat ridiculous, and the methods used to manage info during delays seem to be somewhat spartan!)