Other (great) answers have already covered most reasons.
On Business Jets side, you can do this : http://www.airteamimages.com/dassault-falcon-7x_CS-DTS_masterjet_176224.html
But not that often with airliners. :P
Well, joking put aside...
A third (or second) engine on/below the tail adds specific parts/components, that have to be manufactured, maintained, and spare parts have to be made available for the entire lifetime of the type. Just like the reason why "eyebrows" were removed from the 737 line, and not a single airliner has purchased the 777 with folding wings (and the idea dropped on A380-like projects), reducing costs is a relevant reason to not manufacture "special" parts whenever possible. Best sellers are aircraft that are cheap to handle and maintain. If you can use larger engines to get two instead of three, then...
Similar reasons for unmounting the #2 engine. On a relatively small jet, you can unmount the engine just like it was on the Boeing 727. However, to make that possible with engines the class (and size) of a GE90, you need strengthened structures (increased weight: bad!) around the tail cone, special lifters, a tail cone large enough to contain that engine, compliant with regulation in case of a fan blade failure. Hydraulics and other electrical wiring must be secured. That adds many more special components that have to be checked for airworthiness on a regular basis. When your aircraft is stuck at an airport without the appropriate equipment, you must ferry them there, with the replacement engine. Cost!
It's highly unlikely we'll see a tail mounted engine on airliners the size of a 777 in the future.
Noises and vibrations:
Small engines are OK. Large engines not that much. Even with the incredible progress we have made in reducing engine noise, vibrations are still a major factor, and engine pylons are the best way we have to reduce them. A tail mounted engine doesn't really have a pylon.
Brutally pitching up the aircraft can reduce or disturb the #2 engine intake airflow, with sometimes noticeable issues. This is a major concern for pilots operating on hot and high conditions. This also happens during stall and deep stall. Tail mounted engines requires larger or extra tail surfaces to stabilize the aircraft and reduce drag (weight + more parts to maintain)
When the engines are not mounted in line with the other two (DC10/MD11, Tristar), the center engine produces some specific pitching behaviours depending on loading, thrust and flight phases. It's worse in the case of one inoperative engine. While this behaviour has saved the life of many in the past, it was also a factor in some crashes or close calls.
Related: aircraft behaviour varies greatly between a short version of the frame to a longer one. Stretching a three engined aircraft requires much more research, development and testing than a twin engine one. Having optimized types meeting airlines requirements in your catalog is not that easy with three engined aircraft.
In the case of a component failing at a high rotation speed, a fuel leak, or a fire, mounting the engine in the fuselage is obviously not the most seducing option. The not so distant Qantas A380, Air Transat A330, Concorde in Gonnesse... Fighting a fire on the engine #2 of a Tristar is not the same as fighting the fire on the BA 777 at Las Vegas.
You can't conduct a fan blade overview upon walk around on engine #2.
You can create new nacelles for more powerful, quieter and more fuel saving engines for a 737 (100/200 > Classics > NG > Max > ...) or an A32x (Neo), avoiding the need to develop an entirely new air frame. Reengining the 727 had mitigated results. All KC135 have been reengined and the 747 with the 8I/F. A330 and 777s... Going from the DC10 to the final version of the MD11 (which is basically a reengined and stretched DC10) wasn't that easy. Many retrofits were made available several years after the MD11 entered commercial service. As we don't clearly know what the future is made of, a three engined aircraft may fail to comply with future technologies, which disallows lengthening the lifetime of the type, unless designed from the start to be upgraded, like the Falcon 7X (larger/heavier versions in the plans).
However, having three engines is not a bad thing. It all depends on the purpose of the aircraft. One extra engine can reduce take off roll, allow the selection of smaller and quieter engines (in some rare cases), increase ETOPS certification, give access to hot and high airports, etc. If those reasons are relevant enough to cancel the extra cost required by the extra engine, then you can manufacture a three engined aircraft (or a six engined, like the An225).