In my opinion Rough Guide is the best English language guide on the market. It gives a more balanced and realistic view point, with a great historical and cultural reference section, and is less prone to hyperbole than Lonely Planet. Having taught English in Peru for over six months and having used several guides I would I definitely recommend this for longer stays in the country. It is during longer stays however that you notice some discrepancies between the content of guides and what you experience first-hand, and I have tried to summarise this here.
1) Crime. Reading The Rough Guide advice on crime may make you nervous about coming, especially the advice it gives on Cusco and Arequipa. The book focuses on crime in these tourist hot spots but not, inexplicably, Lima - which is far more dangerous. Although theft can be a problem, normal precautions for travelling in developing countries or big cities apply. There is no need to be overly paranoid about it so long as you keep your valuables discreet (if you need to carry them at all) and don't go exploring any dark alleys late at night. I had no problems with theft over seven months, but I met people who had (but in those instances this was largely due to naivety or carelessness). I think violent robbery on tourists/backpackers is pretty rare.
2) Public transport. The Rough Guide information on long-haul buses is pretty lame. There are a dizzying number of bus companies offering pretty much the same service, and the price is usually negotiable. However, there is only one bus company to my knowledge that offers a direct service to destination, and that is Cruz del Sur. All the others I tried (and I tried many) operated like enormous 'collectivo' taxis that picked up and dropped off passengers wherever they wanted. The buses are often invaded at stops by small armies of peddlers, salesmen, storytellers and beggers. Often we would find, having bought a full price ticket at the bus station, the bus would pull out of the terminal and tout for passengers in the street for half an hour. Local buses in and around Cusco however are efficient and safe, and offer a cheap and effective means of exploring the region. It is not necessary to take a tour to see these sites.
3) Macchu Picchu. All the guide books focus heavily on this, perhaps to the detriment of other sites in the Sacred Valley (i.e, Pisac, Tipon, Chincero, Salinas, Ollantaytambo etc.) which can be reached independently from Cusco. Macchu Picchu suffers from an overload of tourism and hype and can be a let down, especially after the cost of the train or trail, bus to the site, entrance fee and hotel (if you are staying overnight at Aguas Calientes). Expect to fork out around $150 for Macchu Picchu alone - the prices quoted in the guide were quickly outdated and are almost guaranteed to rise again. Of course you are going to go to Macchu Picchu, but don't miss the other sites and villages in the Sacred Valley that offer more opportunities for independent exploration.
4) Food Hygiene. The Rough Guide doesn't make a big enough issue of the terrible food hygiene in Peru. I have travelled widely in the developing world but normal precautions did not prevent some pretty nasty stomach upsets in Peru. There are always some people with the cast iron stomachs that can hack street stall hygiene, but all of my fellow teachers in Cusco were made ill by food at some stage, some of whom had Salmonella and had extended stays in Peruvian hospitals. Take restaurant recommendations from guides and fellow travellers seriously - even an ostentatiously flash, tourist-orientated restaurant can be a risk. Don't be put off eating the raw fish dishes like Cerviche on the coast though - where you will find some of the best, freshest seafood in the world. The fish should have some straight out of the Pacific, and will be naturally cooked in the lemon juice marinade!
5) Desert Coast. Except for Trujillo, Huanchaco, Pisco, Huacachina, Nazca and their surrounding landscapes, there is little to see on the desert coast. It is a poor and industrialised region, and sites of interest are few and far between. For short term trips in the country theses areas are probably not a priority. Some of the Rough Guide's descriptions of the smaller towns were very wide of the mark. 'Chala' for example is described as an attractive little fishing village. It is nothing of the sort. It does get one thing right though - don't under any circumstances go to Chimbote!
6) Jungle. Make sure you pack waterproofs as the tour operators won't advise you to bring them. A torch would be useful too. Don't go skipping around in bare feet and sandles. Small parasites live in the grass and bury under the skin. They then proceed to travel up your leg leaving unpleasant and itchy burrows along the way. This happened to my girlfriend. Literally 'The Green Hell', the jungle is a fearsome but fascinating place, to be taken seriously at all times.
7) LAN airlines. If you are travelling via the States, lock your bag using a TSA-approved padlock. Otherwise lock it anyway. LAN left my bag in Los Angeles and then when it arrived days later there were items missing. This was not an uncommon experience among people I worked with.
That said, it is one of the greatest countries to visit on the planet. Enjoy!