For clarity, various methods have crystallized out over the course of time, as lines can be appropriately grouped or distinguished by the designation.
(Updates for colour coded cargo lines and industrial centers coming soon...)

Because of alphabetic sorting, the first character of a line name has special significance.

Which identifiers you choose and where you distribute them in the line name, is personal taste or depends on your own way of playing. But it helps to think about it.

You can refine the lines as you increase their number, if you have played a map for decades,
Since you will not want to rename a larger number of lines in the future, it is good to use a system from the beginning.

Unfortunately there are no filters in the statistics window. Also with the Linemanager it is only roughly, Even freight and passenger trains can not be separated. What a pity.

First of all, I chose the following identifiers (coming from german, most of them work in English)

B - buses
M - Metro
S - Ships
C - (cargo) Trucks
F - Flight
T - Train

The following subgroups emerged from the game:

BI - Bus interregio
CS - Cargo Ship
CF - Cargo Flight (thanks Gwinda!)
CT - Cargo Train
T3 - High Speed Train

For the local bus lines within the places I use terms like

- B Gotha East West
- B Gotha Airport

or shorter

- B Gotha EW
- B Kiel SN
- B GothaA

For ring lines:

- B KölnCycle (or "RingB" for backwards)

In Interregio bus lines I use start, transit (big) places and destination:

- BI Cologne Kiel Gotha

Or in short form

- BI CologneKielGotha

(If you use line numbers, you can also use even numbers like for North-South and odd for East-West as in German motorways.)

I like to play on big maps (so that high-speed trains can actually drive really fast), in the middle of the map growing cities (which also grow accordingly) with stations as junctions, from which trains travel to different regions more outside.
You could, of course, use pass through (large) places and destination in the line name.
However, if you rarely play or play several maps, you often do not know where the places are exactly on the map. Due to the restricted visibility of the map and the still missing mini map, further orientation is missing. In the end you want to know roughly the direction and the region the train will go.

In the picture above you can see the further geolocale refinement, namely the (rough) direction, into which the line leads and usually start and destination.

In the local traffic, whose area you can overview on screen, but I actually use the passing places. Here, e.g. Regional bus lines:

- BI Cologne Kiel Gotha

Or in short form

- BI CologneKielGotha

A slightly modified system applies to cargo lines, since usually several lines (usually trucks and railway) belong together. My system is not as uniform. 
Mostly raw materials and products are included and because the lines belonging together locally, usually also the city to be supplied is part of the line name:

-C Wood2Saw, C Wood2Saw Kiel (for larger maps contiguous lines will be obvious quickly)

Because sometimes, the end product of a factory supplied several cities, I have used the "<", so food goes to Kiel in the example below. As the cities need different products, you can see quickly which products are missing.

-CT Kiel<food (city supply line)

You read a brief summary of classification which has evolved during years (decades) playing from Simutrans to Transport Fever. 

I hope I can give you some suggestions. You're invited to provide suggestions, complaints and supplements, I will add your ideas.

A Pleasant Journey,
Rolf

PS I am not a native english speaker as you see, so feel free to correct me!