1. Have them properly (read:professionally) installed.
My husband and I aren't really good at building or nailing or screwing in light bulbs or unclogging the toilet, so we knew that we'd have NO idea how to properly install a window unit. Some people feel totally comfortable doing this. I will say the following. If you live on a higher floor or the window you are installing a window unit into is above a sidewalk I would highly, highly recommend paying someone to install the unit for you. If it falls out of your window you will be responsible for the damage incurred as a result. Also, and perhaps more of a motivator, you will probably either seriously hurt or kill someone. Maybe a small child, maybe a baby. Please, please only install your own window unit you are 199% CERTAIN that you are doing it properly. Keep in mind that birds frequently land on the unit and can add a significant amount of weight to the unit. Another thing is that one of the windows in our apartment was really wide. So wide in fact that the "wings" that come with the unit designed to fit inside the widow were not big enough. Our installer had to cut plexiglass in to fit the space not covered by the wings. I don't know how I would've remedied this problem if we were doing it on our own.
2. BTU
Do a little research and find out how many BTU's you need. Any website selling window a/c's should have a guide to how many BTU's you need . I know our 12,000 BTU unit supposedly cools a room that is 500 sq feet, but I ended up getting one 12k BTU unit for the living room that is 140 sq ft and one for the bedroom which is also about 200 sq ft. I thought maybe I had gone a little over board, but my installer said I was so smart to pick those because they are way more efficient and cool your room very quickly. I also purchased a smaller 5000 BTU unit for my other bedroom and I have to keep that one all the time in order to just keep the room cool. Another reason I went with the larger a/c units is because I found them for a really good price. I think is spent $199 on each one and similar smaller units ran for close to the same price. I chose J and R in NYC by chance and picked up the units on my first day in, after signing our lease but before we went to IKEA. There are delivery services you can use, but I just found this to be the cheapest option. I don't regret it, but now that I'm more versed in the city, I probably would have arranged for them to be delivered.
3. Filter
You need to clean the filter every 2 weeks. This just involves pulling out the filter and running it under the facet in the bathtub. Then, you just let it dry for a few hours. This is the single best thing you can do to reduce your electric bill during the summer. Remember that these filters are somewhat delicate, so handle them accordingly.
4. Choose a good installer
We called our door man for a recommendation, but if you google a hardware shop near your apartment you should find someone to do it. You need to know the size of your a/c and the size width wise of the window you're planning to install it in. I think we paid $125 for the largest window, $85 for the other window that didn't need any plexiglass, and $65 for the smallest unit.
Now a word on buying used a/c's. In a later post I discuss buying used items and how wonderful it is. The reason I didn't buy a used a/c is simply because I didn't want to have a big time lapse between when I moved into my apt and when I had an air conditioner. Also, since they can be very heavy you have to take into account that you'll be moving it without a car. Of course you can pay for a cab, but you might end up having to take the subway all over to find an a/c only to discover it's not in great condition. I, for one, have taken excellent care of my units. They are impeccably clean and cared for. However, I will likely move with them because I know prefer them to central a/c. Only cool the room you're using and do it quickly.