Hi, Psylow, I'll take a stab at it.
As your question suggests, there are different materials for different kinds of seams or gaps.
For seams that are visible but otherwise relatively tight, that is, you can see 'em, but you couldn't fit a piece of paper into 'em, I'll try to avoid creating them in the first place. Take 2 halves of a fuselage, for example. I'll use liquid cement to join the parts, and squeeze them gently, so as not to distort the shape, but enough to let the melted plastic extrude along the seam. When the glue cures, you can scrape that bead of plastic away and have a clean seam that can be lightly sanded and disappears easily.
I'll also use putty thinned with acetone, for seams like this. I use two methods. I will apply the putty to the seam, using a toothpick, or flat blade, removing the excess, and then using a cotton swab dipped in acetone, I remove the remaining excess putty, leaving only putty in the seam. When this dries and cures, it can be sanded smooth. Or I will put a blob of putty on my palette (any impermeable surface will do) and add acetone with an eye dropper, and stir with a toothpick, till it's a thick liquid. I apply this to the seam with an old paintbrush. (I call this "homemade Mr Surfacer"). Let it cure, then sand.
I will also use Mr Surfacer on seams like these, but I found that it was easier to use thinned putty.
On gaps, where you can see daylight because parts don't meet quite right, I've used putty, on narrower gaps; stretched sprue and liquid cement; styrene card slices and liquid cement; or combinations of putty, styrene pieces (on styrene kits) or bits of resin casting blocks and putty. The plastic or resin pieces help fill the gap, and the cement or putty helps hold it together.
I have also used wood putty (Elmer's) on some of my metal figures, sometimes hardening it with a shot of CA glue.
Hope that helps!
Brad