Most people have mentioned the level of cleanliness for a TOC in general, so I thought I'd mention a particular line.
The St Albans Abbey line has to be by far the dirtiest that I've been on, both inside and out.
Outside the the train is usually caked in dust and mud, with various references to it written in the dirt such as a crudely drawn name plate saying "Grot box"

.
Inside, there are used tickets chucked about and torn up like confetti, various drinks containers and crisp packets scattered around the seats. It's generally unpleasant.
I know it is down to the fact it simply goes back and forth all day, but the Marston Vale trains seem cleaner and are operated by the same TOC. Maybe it's the clientel, or maybe more cleaning staff are used for it. I'm unsure anyway.