There are three things that determine sound quality:
1) The thing interpreting the sound (your brain - via your ears)
2) The room in which the speakers are being used
3) The thing producing the sound (the speakers - driven by an amplified source signal)
The order in which I've listed those three things is also the order of importance.
The first thing you have to know is: how is your hearing? Most of us have some hearing loss. We all lose some of our hearing sensitivity as we get older, but by no means do we all lose our hearing to an equal degree or in an equal way. Ask you doctor for a referral to get your hearing tested. It's an interesting experience. I like to get my hearing tested every few years or so.
I recently went and got my hearing tested. I'm 27 and I take some care to try and protect my hearing, but the recent test showed that I'm really not hearing much above 16.5 kHz anymore. Furthermore, I have some hearing loss in my right ear, but not my left ear. I had an ear infection in my right ear - it's likely the cause and culprit for my hearing loss in that ear. It's not severe, but I do have some hearing loss in the treble frequencies in my right ear.
Why know this stuff? Because it's all fine and dandy to go on and on about flat frequency response, anechoic frequency response, +/-3dB response, blah, blah, blah - but ultimately, it's my ears that do the listening - not some frequency response graph - and if my ear do not have flat frequency response, I need to know that so that I know
why I'm hearing what I'm hearing.
So in my case, there's a good chance I'd prefer speakers with a slightly tipped up high end. I know that I have some hearing loss in the highest frequencies, so I know beforehand that a truly ruler flat speaker isn't going to
sound ruler flat to me.
Once the most important factor (your own hearing) is known, it's on the analyzing the room. It's the room that determines the frequency response that actually reaches your ears. The sound may come out of the speakers ruler flat, but once it interacts with the room, what actually reaches your ears is totally different!
There are a number of ways to deal with your room. You can hire a professional to come to your home with some rather expensive test equipment. He or she will take real time measurements and acoustically map your room. This costs a pretty penny though and any time you move anything, it changes all of the measurements! So unless this is a truly dedicated room and you are really prepared to make the investment, hiring a professional is usually beyond the price an average person would want to spend.
On the opposite end of the spectrum are the built in "auto room correction" programs built into receivers. Programs such as Audyssey's MultEQ or Yamaha's YPAO or Pioneer's MCACC. Some of these actually do a pretty decent job, but you are more or less at the mercy of the built in programming.
A new technique that is emerging though is that companies like Auralex and Ready Acoustics are offering real world measurement in the lowest cost form possible. Auralex is about to launch this new service - Ready Acoustics is already doing it. Basically, they send to some test tones and give you some suggestions on what microphone to use. You connect the mic to your laptop, run the test tones and send all the data back to the company. They analyze it and report back to you with an overview of your room's acoustical map and suggestions on how you can improve the acoustics in your room using their acoustic treatment products. I love the idea of this service
After you've taken care of the two most important aspects - your own hearing and the room - the speakers you chose to create the sound are almost an after thought.
There's no hard and fast rule as to whether towers are better than bookshelf speakers or vice versa. In most cases, it's really only a matter of how low you want the speakers to be able to play before they cross over to a subwoofer. I am personally in strong agreement with THX in the suggestion that you cross over the speakers to the subwoofer at 80Hz. If you go along with that suggestion, tower speakers are typically not necessary.
Tower speakers can also typically play louder - simply by virtue of having more and/or larger drivers and having more cabinet space for greater air movement and resonance. Most of the benefit of being able to move more air has effect on the mid-bass and bass though, so once again, if you are crossing over to a subwoofer at 80Hz, it makes much less difference. A good portion of the mid-bass though is still handled by the speaker. In a very large room, a bookshelf speaker may struggle to reproduce the 80Hz - 300Hz range with enough loudness for the room size. In that case, a tower speaker would likely be the better choice.
So once again, it is the room's size that determines the choice of speaker. Regardless of the room's size, I would recommend using a subwoofer. Bass frequencies are the most prone to drastically altered frequency response due to interactions with the room. In my opinion, it is vital to be able to position what ever speaker is producing the bass in the position that is closest to ideal. It is typically impossible to accomplish this goal if you are running the main speakers "full range". You are bound by the desire for a good soundstand and imaging to position the speakers in a certain location at the front of the room. But this is typically not the best position for bass response. So instead, it is best to seperate the bass and allow it to be produced by a subwoofer that can be positioned in the ideal location while the main speakers remain in the best position for soundstage and imaging.
Best of luck!