In regards to the panel lines on aircraft; most modern aircraft have very tight joints between panels and the individual panels that make up the airframe are not actually visible. We expect that our models should show this "detail" which in fact does not exist. What many people think of, as "panel line is really differences in the way that the paint fades the panel lines that will show are those that are accessed often: gun bays, some avionics bays and fuelling access panels. That kind of stuff.
Airliners are very similar, except the panels will be such things as lav access, potable water, and external power. Things like that your best source of information is to look at actual aircraft. That being said, I have several methods:
Paint the model in the final coat and apply a "wash" of paint touched into a panel I want to highlight. Capillary action will cause the paint to "run" down the panel line. The excess paint can then be removed from the surrounding area. Water based paint is good for this as it can be cleaned off with water before it dries. Enamel or lacquer works too, but the excess is harder to clean up. Oil based paint thinned with turpentine will also work, but that method is best if you have a gloss finish to work with. To highlight the panel line, but not over emphasis it, it is best to use only a slightly darker shade.
(Requires and airbrush) Use a straight edge along the panel line (ruler, piece of card, etc.) and lightly spray a darker color at a very low angle from the straight edge. This can add a very subtle difference that is convincing with enough practice.
Paint the darker color along the panel lines first, and then apply the topcoat a little at a time. I have done this with an airbrush; don't know if it will work with a brushed-on finish.
On many Navy aircraft, touch up paint is sprayed over "dings", wear and tear on the paint, and other flaws in the finish. From a navy mechanic's point of view, paint is applied to protect the airframe from corrosion (and rightly so), so matching the color is not that important? Many times the paint is not mixed thoroughly, or does not match exactly for some other reason, so the finish is kind of "spotty". A friend refers to this as "Corrosion control camouflage". It is best replicated with very subtle differences in the shades of paint. Again, practice will perfect this on a model.
Many stains on the exterior of an aircraft are due to hydraulic leaks and seepage, fuel spills and stuff like that. Slats and flaps can have (and usually do have) stains, though they usually "run" in the direction of airflow away from the joint. Most modern military (well, commercial too for that matter) have single point refueling. Usually under the wings! Air to air refueling can result in a fine mist that looks like a dusting of clear gloss on the top surfaces.
The photo-etched parts that you asked about are best cut off on a flat surface using some sort of sharp knife blade (Exact, or something like that). When I have tried to use side cutters, I can't cut close enough to the part and usually end up bending it in the process. For corners use a straight edge or some sort of form to bend the parts over.
Fortunately most photo-etched parts on airplanes represent flat parts, so bending them to fit is not really an issue. To glue them to the model use some sort of cyanoacrylate like Super Glue, or Crazy Glue. Make sure all the bonding areas are free of paint, or the glue will not stick.
I hope this is not too confusing; I have been distracted by two F-15s and a B-1 that are arriving here for an air show. They seem intent on blowing the shingles off of my roof.