Um. Since the Railways Act 2005 emasculated the former Rail Passenger's Consultative Committees, you're a bit stuck*. There's the Office of Rail Regulation, who are only interested in the amount of public subsidy, your MP, who may or may not be any good, your local press (who may already be aware) but the official watchdog are this bunch:
http://www.passengerfocus.org.uk/
who are fairly toothless, but give them a go. Bear in mind that delays might actually be Network Rail's fault, not LMs, although most new franchisees seem to have teething problems. NR are almost completely unaccountable to anyone, having a single mission to save money.
* The point of the Act was to reduce the Government's subsidy, by shoving it onto the farepayer. Naturally, strong passenger's representative groups are incompatible with this, so they had to go.