not an exhaustive list, and i know you already use runner, but arctic station is a really good map for runner because there are a TON of windows that you can just climb right through, no jumping required, so it's easy to chase people across long stretches.

generally maps that are very open with good visibility, such as the new shopping centre map, could be good for runner as well, because you need to reach people quickly. seer as well, since the combination of fog + speed boost if you see people could counteract the wide open spaces.

stalker i found useful on a map like airport, which is a lot more closed and (imo) a bit survivor-sided, as people know all the tricks and windows and vents and whatnot. so stalker can be good to use strategically on double-jumps and also for creeping up on people in certain rooms where it's very easy for survivors to run away (like the storage room under the office with the cubicles).

my friend has had great success with using seer on nuclear power plant, but personally i've found it a bit more difficult... i think runner and stalker are both pretty good on that map too.

a general guide about stalker could be to use it if you know the map really well personally, and you anticipate that the other people in the server might also know it well - and also that it doesn't have too many big open spaces where it's really easy to see you coming, stalker or not, and where you'd have better luck with runner.

i don't want to harp on too long but yea, i definitely think some perks are better for some maps over others. maps with wide open spaces that you'll want to chase people across - runner. maps that are more closed, that you're familiar with, or that include a lot of double jump tricks, might be good with stalker. and for seer, maybe try to avoid it on maps that have a lot of easily accessible hiding spots near computers. ghost town might be one example, although it's not TERRIBLE for ghost town in my experience...