Accomodation

Best location
    If I was travelling to Lisbon I'd know where to book my hotel: somewhere near Rossio square. This is the exact centre of the city and at a walking distance from almost all attractions (except Belém area, which is far from everything) and being there you don't need to worry about transportation, the time you take to go to the centre or anything like that. Besides, it makes everything easier to find a good restaurant close to your hotel or to go for a short walk after dinner.
    If you're afraid of hearing too much noise during the night, Avenida da Liberdade may be a good option: 5 walking minutes away from Rossio, still close to everything but more quiet and most hotels have double windows, which should keep the few noise away.
    In both cases you'll be 20 minutes away (by taxi) from the airport, so, there's no need to book an hotel close to the airport for your last night.

Worst location
     Avenida Almirante Reis and around. Looking at the map it seems really close to the centre (and is) and I bet you're finding excellent deals in that area... but maybe those hotels don't expect you to stay the whole night, if you know what I mean. Most structures are old and you won't feel much safe if you try to walk to your hotel at night, plus, subway closes earlier in that area.
    Bairro Alto: close to the centre, no security problems but is the area where all the nightlife happens: double check if the hotel has double windows or you won't sleep until the last person goes home.

Traditional neighborhoods

     Alfama, Graça or Castelo may be a fun alternative and give you a local's view of the city and it's life. Though there aren't that many hotels, there are apartments to rent for tourists, easy to find and book online. To my opinion, they are great if you're staying for several days. If you want to feel integrated do yourself a favour and greet your neighbors when you pass by, you'll be surprised with their kindness.

Pousadas
    Some kind of state-inns, they are a different kind of accommodation, located in very special places. In Portugal there are 40 different pousadas, divided by 4 different categories: charm; historical; historical design and nature. Staying in a Pousada you'll have the opportunity to sleep in old palaces, former monasteries and special places like this.

Check-in and Check-out: by law, all kinds of hotels and accomodation providers should give their costumers the room from 2p.m. And for the same reason, you should leave the room until noon of the check-out day.
If something goes wrong you should ask the "complaints book".