It depends on the champions and what I want to build.
I never bother with CDR runes on Jayce since I will generally be fighting early (so I need MR in mid-lane) and my core items provide 40% CDR anyways (Ionian Boots, Muramana, Youmuu's Ghostblade, Black Cleaver).
However, certain champions are generally safe enough that they don't need MR and don't want to build certain items for it.
I generally take 20% scaling CDR on long-range champions such as Lux and Varus since I generally won't be fighting early-game (instead trying to farm for the mid-game). As such, I can generally cap my CDR with one or two core items:
- Lux: Morellonomicon or (Ionian Boots and Zhonya's Hourglass)
- Varus: Ionian Boots and Youmuu's Ghostblade
That said, I have 20 rune pages and pretty much every useful rune so I have plenty of flexibility in my set-ups.