Minitour,
Your observation about the different procedures is quite accurate. There are many reasons why this happens but I think they can be narrowed (basically) to three concepts.
1. As JAFI pointed out, there are a wide variety of "options" available in transport category aircraft that you don't usually encounter is small aircraft. They are too numerous to list, but may include such things as different cockpit layout (based on the buyer's choices), different fuel tanks, capacities, locations, different flap positions, different weight limits, completely different avionics packages, different cabin options (emergency lighting, equipment, etc.) and so on. These items can result in the need for different "procedures".
2. Factory provided "checklists" are written by lawyers, with input from pilots/engineers (not the other way around). More often than not, the "procedures" they contain are designed to protect the manufacturer from liability, rather than provide for efficient and practical safe operation of the equipment. If they were followed in the "way they come", everyday operations in the real world would come to a screeching hault. They are often extremely redundant, have no logical "flow patterns" and would cause more problems than they fix.
Mature airlines have people who review these procedures and rewirite them so that they work in the real world. The modified procedures that result do NOT omit anything that is essential for safety, but they do throw out the impractical junk, and organize the material into more useable and practical sequences. A Before Takeoff checklist that takes 20 minutes to complete would literally shutdown the "system".
Since this (rewrite) is done by different people at different airlines, they don't always come out "the same". However, they all "get the job done" and they are all ultimately "approved" by the Federal authority. Sometimes extra or different items are "included" or "added" based solely on the whims of a particular POI (prinicipal operations inspector) from the FAA. Some airlines fight these POI's when they disagree with them. Other airlines just don't make waves. End result = different procedures.
Immature airlines are usually "afraid" of the POI (FAA) or don't have the inhouse expertise to develop their own procedures. So they just go along with whatever junk comes from the manufacturer's lawyers (just like Private pilots and part(s) 91 and 135 operators).
In most cases you will find many variants in the "normal" procedures, but NOT in the emergency procedures. Most airlines, particularly the smaller ones, are reluctant to take on the expense of changing emergency procedures and getting them approved. Remember, the airlines have "lawyers" too and usually they are more interested in protecting their carrier from liability than changing a not so good procedure to a very good procedure. As a result, some Emergency Check Lists found in QRH booklets that "come with the airplane" are literally an "accident looking for a place to happen", but remain unchanged. They often increase workload at the most critical of times and require back-and-forth cross reference to different sections of the QRH, or are [shall we say] less than clear.
One area of particular concern is "memory items". When emergency checklists are modified this is usually where you'll see the greatest differences. This is a matter of "philosophy". Some people think it's great if you can "memorize" everything. Others (like me) think that "memory items" should be reduced to the bare minimum. Arguably, memory is the weakest link in the system. The more you have to do from "memory", the greater you chance of forgetting (making a mistake). Example: Some engine fire checklists might include 10 memory items (or more). Others will include ONE memory item --- turn off the [dam_n] bell.
In most cases, only the big airlines with their own "engineering" departments and much expertise among program managers for the aircraft type will "take on" the powers that be and get a bad emergency checklist changed to a good one.
The "net result" of all this is different procedures, in different companies for the same aircraft model.
3. Finally there's the ego element that you touched on, i.e., "I know more than you and we can do it better". While this may sound "far out" when you first look at it, there are some cases where it is true, i.e., some folks DO "know better"; particularly when "experience" with the type is the cause of changes made over time.
A company with 10 737's (your model choice) is not usually going to be changing much and sticking its neck out. On the other hand it could be argued that nobody anywhere, including at Boeing, knows more about how to operate a 737 than SWA. With such a large fleet of the same basic type, including most of the many variants, they have a level of "expertise" that is difficult to match. Because of this, they may very well have "procedures" in the cockpit, it maintenance, etc., that are substantially different from other operators.
In similar fashion, a 747 operated by say NWA or UAL is not likely to be "run" in the same way that a 747 opreated by say Atlas might be run.
In any case these "differences" boil down to a matter of opinion and are often more subjective than objective.
When one is forced to change airlines or does so voluntarily, we need to recognize that the new company pays you to fly their airplane, their way. The best thing you can do as a pilot is to leave the "we did it this way at XXX" behind you and learn how to do it whatever way your new employer requires. Unless it's a glaring issue involving the safety of flight, you'll be way ahead of the game if you just do it "their way".
One last thought: Be careful not to confuse "technique" with "procedure". These are two different animals. There can be W_I_D_E differences in technique and that's OK. The differences in "procedures" are usually small by comparison. Technique can be changed by the pilot. Procedures must be followed.
Someone said: There are 3 ways to fly (do everything) every airplane: your way, my way, and the right way. The first two are a matter of opinion and yours is just as good as mine. The third (if known) is the one to follow. Why? Because ....... Failure is NOT an option.