I guess Manu must be visited on a tour (particularly if I want to go deep inside the park).
Tambopata and Arequipa areas seem good places for independent travel...
What do you think? Where is it possible to do it independently (alone) and were do you think it is required to go on a tour?
Any tour operator suggestions? What about Kolibri expeditions? Inka Natura? Manu expeditions? They seem to be the only tour operators offering a stay INSIDE Manu...
Only scientists and alike can visit the main section of the park. A few sections are open to tourists, but only with guides and permit (which you shouldn't worry about if going with an established company, as they'll deal with that). Some of the neighbouring regions (e.g. Manu road and associated lodges) are often referred to as Manu, but are actually not within the national park itself - these can be visited alone, though some lodges in the lowlands can be difficult and/or expensive to reach alone, as they typically require a boat. Tambopata really isn't any different - you can't just walk into Tambopata. Most transport is by rivers. If your Spanish is fine, boat-transport can be arranged fairly easily independently, though - at least if alone - you'd be hard pressed to get it cheaper than what the various lodges and tour-companies offer. Tours to both Manu and Tambopata are sold widely in Cusco, while tours to Tambopata also are sold in Puerto Maldonado. However, if not knowing a bit about the lodges they offer beforehand, it can be a bit of a hit-and-miss (as a very rough rule, the further away the lodge is, the more pristine the habitat is... and the higher the price is). For this very reason, none of the lodges found further within lowland Manu and Tambopata are places where you just turn up and get a room; they typically require reservations beforehand (however, most of the lodges have an office in Cusco and/or Puerto Maldonado where you can enquire - many also have web-pages). Additionally, if just taking a random tour sold in Cusco or Puerto Maldonado the chance is you'll end up on a tour with "normal tourists", which couldn't care less about the small antbird you just saw, and certainly won't stop for a second look at it. So, it really depends on you and the time you have available. If missing a day (due to "South American time") isn't too important for your itinerary, and you can utter at least a few phrases in Spanish, things like Manu road and Arequipa (tours to Cañon del Colca are sold in Arequipa, but just getting on a bus is easy, too) are straight forward. Lowland Manu (-region) and Tambopata are a bit more problematic and require a bit more work, but can be done. Another thing to keep in mind is that guides also can be helpful with bird ID's, especially if not already familiar with Neotropical birds. Much Neotropical birding is done by ear, i.e. unless you've been doing a fair deal of practicing before you leave, many species will be missed. Some species (many antbirds, antpittas, tapaculos, etc) are also highly unlikely to be seen without play-back - most guides and Neotropical birders use it at least occasionally, but some won't due to the possible issue of disturbance. Regardless, this is only really an issue in forest areas (Manu Road, Manu, Tambopata, etc), and of no real relevance for most open-country birds (e.g. near Arequipa and Paracas). A bit on Puerto Maldonado, incl. a few lines on Lago Sandoval, can also be found here - written several years ago, but still fairly accurate:
http://www.birdforum.net/showthread.php?t=30692
Regardless, I'd recommend getting a copy of Thomas Valqui's
Where to Watch Birds in Peru - a few things have changed since it was published, but overall it's still an excellent resource and certainly a must for any birder even considering doing Peru independently. Of course also the new field guide to Peru, which is far more useful than the old.
