In East Anglia - where passengers have been plagued by problems over recent weeks - a broken-down train meant there was no service between Ipswich and Felixstowe, with buses having to operate in the morning rush-hour instead.
There were also hold-ups due to signalling problems between Bedford and Bletchley and between Selhurst, Norwood Junction and West Croydon in south London. Words: PA
Another south London problem in the shape of emergency engineering works between Clapham Junction and Earlsfield meant disruption to a number of services in and out of London's Waterloo station.
It was over-running Christmas engineering work at another major London terminus - King's Cross - that led to the station being shut on Saturday, sparking chaotic scenes there and at nearby Finsbury Park station.
While NR expressed regret for the over-run, Transport Secretary Patrick McLoughlin described the situation as "totally unacceptable".
The travel chaos has thrown the spotlight on NR's bonuses for top executives. The company has scrapped its long-term incentive plan for top bosses but still has in place an annual performance-related bonus for the chiefs.
Although this annual bonus is limited to 20% of salary, the scheme would still entitle NR chief executive Mark Carne, who is on a salary of £675,000, to a bonus of up to £135,000.
Mr Carne is not entitled to the long-term incentive plan bonus for which 2014/15 is the last year.
NR's network operations managing director Robin Gisby, the man masterminding the Christmas engineering work programme, is also not getting the long-term bonus, which could have been as much as £371,000, as he is leaving the company at the end of February.
Whether the top directors get their bonuses for 2014/15 or not will be up to NR's remuneration committee.
There have been pleas in the past by politicians and by the Office of Rail Regulation (ORR) for the remuneration committee to take more heed of poor performance in their assessment of bonuses.
With NR's debt now officially on the Government's books there will be more pressure this year on the committee.
The ORR has launched an inquiry into the Saturday chaos. The ORR could, as it has in the past, fine NR for over-running festive engineering work.
However, critics of the whole rail set-up are quick to point out that with NR being a not-for-dividend company with no shareholders, any fine imposed on it is effectively paid by taxpayers.
The travel chaos at the weekend was merely the latest in a series of late-autumn, early-winter disruptions to services. Some have been down to the train companies, with a number of trains breaking down. But most have been due to signal failures which are down to NR.
On Friday, passengers' mid-winter misery will be compounded by the annual fare rise which will see season tickets going up by up to 2.5%.
Mr Carne has, reportedly, been on holiday in Cornwall over Christmas. An NR spokesman said that Mr Carne was "at work" today but it was unclear whether he was working from Cornwall or from NR's London headquarters.
Asked whether Mr Carne was working from his office in London, the NR spokesman said: "He is working in an office."
The spokesman went on: "He is at work. He has been working throughout, overseeing all the work and also the problems we have had."
The UK's worst train stations
More rail delays amid bonuses row
This Edwardian station was built in the early 1900s and is operated by East Midlands Trains. 59 per cent of people surveyed said they were satisfied with the station - a low score which ranked it bottom for both cleanliness and facilities in the Passenger Focus National Passenger survey.
Birmingham New Street railway station is the largest and busiest serving Birmingham. Despite the regular flow of people, only 64% of passengers surveyed in the National Rail Passenger Survey (NRPS) are satisfied with the sation.
London Bridge railway station is a central London railway station and a London Underground complex in the London Borough of Southwark. The station is the oldest railway station in central London and one of the oldest in the world. 67% of passengers surveyed were satisfied with this station, the fourth busiest station in London.
Peterborough railway station is a major interchange serving both the north-south ECML, as well as East-West long-distance and local services. The station is managed by East Coast. Just 67% of passengers surveyed were satisfied with this station.
Crewe station was completed in 1837 and is one of the most historic railway stations in the world. Like London Bridge and Peterborough, only 67% of passengeres surveyed were happy with this station.
Gatwick Airport station provides a direct rail connection to London. The station platforms are located about 70 metres away from the airport's South Terminal. 69% of passengers surveyed were satisfied with this station.
Stockport railway station was identified as one of the ten worst category B interchange stations by a mystery shopper assessment in 2009. Despite improvements being made to the station since, it is still one of the ten worst stations with only 70% of passengers satisfied with the station.
Clapham Junction station is one of the busiest in Europe by number of trains using it with many routes from London's two busiest termini, London Waterloo and London Victoria. Only 71% of passengers surveyed were satisfied with this busy station.
Maidenhead railway station serves the town of Maidenhead, Berkshire, England. It is served by local services operated by First Great Western from London Paddington to Reading, and is also the junction for the Marlow Branch Line. The survey showed 71 per cent of respondents were satisfied with the overall quality of the station, giving it the ninth lowest satisfaction rating.
Coventry station has the PlusBus scheme where train and bus tickets can be bought together at a saving. Despite this convenient feature, only 72% of passengers surveyed were satisfied with the station.
The line between Glasgow and Mallaig is one of Britain’s most eye-catching train journeys. During the course of the 164-mile route, the “Road to the Isles” hugs the banks of Loch Lomond on departure from Glasgow, before making its way past castles, mountains (including Ben Nevis) and waterfalls en route to Scotland’s west coast. Then, just as you approach the journey’s end, the track crosses the spectacular Glenfinnan Viaduct, made famous by the Harry Potter movies.
There’s no disputing the Cote d’Azur is one of Europe’s loveliest coastlines, with golden beaches and bright blue waters stretching for more than 100km. Skirt the shoreline from Fréjus in France to Ventimiglia in Italy and you can give this sandy playground a closer inspection, because there are ample opportunities to stop and soak up the atmosphere if you catch one of the daily regional TER trains, which call at Cannes, Antibes, Nice, Eze and other stops along the way.
Keep your eyes on the skies on the daily InterCity from Venice to Munich, which weaves through the mighty Alps on the Austrian-Italian border. Following one of Europe’s great trade routes, the train calls at some of Italy’s finest Renaissance towns, before continuing to Innsbruck via the Brenner Alpine pass. The section between Verona, Bolzano and Fortezza is particularly striking as the train traces the river Isarco north in the shadow of the Dolomites, briefly crossing into Austria before arriving into Munich in time for dinner.
The narrow-gauge railway from Nice to Digne les Bains, in the Alpes-de-Haute-Provence region, is a relative unknown in the world of scenic trains. A 90-mile journey taking around three hours, it crosses rivers and passes through enchanting communities such as St Andre les Alpes and Entreveux. This is a private railway, so it often remains undiscovered unless you’re on a tour. However, it’s open for exploration by independent travellers, too, departing Nice CFP station four times per day.
A train trip doesn’t need to be long to be beautiful. The stretch from Messina to Catania in Sicily takes just 90 minutes, but the views of the coast and Ionian Sea are something to remember. If you’re travelling overnight from Rome, you’ll wake at daybreak to find the train being loaded onto a ferry. And from the moment you’re on Sicilian shores until your arrival in Catania you’re spoiled for choice – look east to see the rocky Mediterranean coastline and bobbing fishing boats, and west for none other than the peak of Mount Etna, Europe's tallest active volcano.
The joy of train travel is the transition from one place to another, watching the landscape unfold before you as you cross borders by rail. Starting out in Zurich’s cosmopolitan centre, this train quickly ascends into the Swiss Alps, passing green lakes, quaint villages, and snowy peaks. Just a few hours later you’ll descend into Italy, to the shores of Lake Como, catching a glimpse of the cupola of the cathedral and the lakeside villas bounded by Cypress trees. The Zurich to Como route is done on an everyday InterCity train, with no panoramic windows or fancy title to its name, yet it’s still a stunner of a trip.
The Golden Pass refers to the stretch of railway from Montreux to Lucerne in the Swiss Alps. Though feasible in a day, the route isn’t one to conquer in such a short time, and should be savoured. With countless opportunities to get off and explore, it’s easy to build your own itinerary on Switzerland’s famous scenic railways. The region is home to a host of scenic services, including glass-topped panoramic trains and funicular railways, so it’s little wonder that the Oberland attracts such wide praise from train travellers. Between Lucerne and Interlaken the landscape is exceptionally beautiful, passing the emerald-green waters of Lake Lungern and lakeside hamlets at the Brunig Pass.
Travelling at around 20mph, this scenic train is the epitome of slow travel. But although the Bernina “Express” hardly deserves its title, as it winds through the southern Alps, over bridges, gorges and precarious mountain passes, you wouldn’t want it to go any faster. Crossing some 200 bridges and passing through mountains via 55 tunnels, this is a feat of engineering so impressive that it has earned Unesco World Heritage status. The panoramic train has been designed to offer a ringside seat and as the rails mount the Albula pass to St Moritz, you won’t be disappointed by the views.
Fjords, glaciers and snow-capped peaks provide the spectacle on the Bergen Line, one of Scandinavia’s most impressive train journeys. Travelling from Oslo to Bergen in around seven hours, the trip’s highlights include Europe’s largest mountain plateau, Hardangervidda. But it’s not just the views that impress; the railway itself is extraordinary. More than 15,000 men laid this track into the peaks and dug 182 tunnels out of mountain rock, by hand. Construction started in 1875 – and took 34 years to complete.
An unexpected beauty in Spain, the train between Madrid and Oviedo offers a glimpse of classic Spanish countryside on its way from the capital to the north coast. And as the train approaches the Asturias region, and its principal city Oviedo, it climbs into the clouds, passing through the Picos de Europa mountains. Upon arrival in Oviedo, the train remains the best way to continue your explorations of the area: take a Feve narrow-gauge railway to Galicia and the Basque Country.