How to deal with magma cubes in the Nether?

Solution 1:

There's an oddity in monster spawning you can exploit. As is well known, mobs can spawn on top of any block with a flat, opaque top surface, even if there is a non-solid block such as a torch or rail on top of that block.

However, the selection of center points for groups (“packs” as Minecraft Wiki describes them) of mobs is slightly different: it requires that there be empty space which is an air block, nothing else (not even a torch). Only once such a point has been found will mobs spawn with their feet at that level in the area around that point.

Therefore you can prevent spawning entirely as follows: make sure that in the vicinity (up to 20 blocks horizontally) of your rail station, at any particular y-level, either there are no empty air blocks, or at the y-level below it there are no regular valid spawning surfaces.

For example, consider this cross-section of an underground rail tunnel.

5  #########     _ slab
4  ###   ###     # stone/netherrack
3  ###   ###     R rail
2  ###R_R###     
1  #########

No mobs can be spawned in the middle of a tunnel of this form:

• No mobs will spawn with their feet at levels 4 or 3 because there are no solid blocks below those levels (all individual spawn locations are invalid).
• No mobs will spawn at level 2 because there are no air blocks at that level (all pack spawn locations are invalid).

However, if there are any air blocks at level 2 within 20 blocks of the tunnel, then they may cause spawning. So, if the tunnel is in midair as such things often are in the Nether, you'd have to build a 20-block-wide flange beside the tunnel at level 2 to prevent spawns (preferably made of slabs so as not to itself be a spawning platform).

Disclaimer: I've never tried to engineer spawns in this way; I'm just going by others' documentation of the way it works. (And yes, this was already mentioned in the comments of this question; but answers should be posted as answers, and I felt a fuller explanation would be useful.)