Thousands of commuters were facing delays on their journey home after major disruptions on both the London Underground and on trains.
The Central Line, which has some of London's busiest Tube stations, was shut because of signal failures and has since been experiencing severe delays.
There were also severe delays on the Circle Line and Northern Lines due to late-running engineering work.
Bad weather caused trains heading into most overground stations to be delayed.
The Central and the Circle lines are maintained by Metronet under the private public partnership (PPP) scheme for the Tube.
The company apologised to customers for the delays.
It said the Central Line delays were the result of the loading of new computer software containing LU's revised timetabling information which caused a total break-down of the systems.
The District and Circle lines were delayed after weekend work on the track between Cannon Street and Tower Hill overran, leading to the late reopening of the lines.
A signal failure on the Northern Line also added to delays on the Tube.
Last week, PPP arbiter Chris Bolt published his report into Metronet's performance from 2003 to 2006.
He said the company had not performed in an economic and efficient manner or in line with good industry practice.
The Rail Maritime and Transport (RMT) union said Tube infrastructure work should be brought back in-house before the entire system "ground to a halt".
London mayor Ken Livingstone said: "Metronet have entirely unnecessarily ruined thousands of Londoners' journeys this morning."
At least 60 Metroline bus routes across London were also affected on Monday because of a 24-strike over a pay dispute, causing disruption for many bus passengers.
London Assembly transport committee chairman Geoff Pope said: "With the triple whammy of a strike on the buses, late-running engineering work and signal failures, it has been a miserable Monday for thousands of Londoners simply trying to make their way to work."
High winds and rain had resulted in many lines being affected by leaves on the tracks.