Blue M.pen runes ?

They seem a bit lackluster as opposed to MR/level (or flat) or CDR/level glyphs.

You mean Glyphs? No.

Typically you want Scaling CDR or Flat MR or Scaling MR.

Scaling AP is another decent option, but not one I recommend.

I wouldn't use them. CDR, MR, or AP seem to give a good bit more per rune than Magic pen does.