Your suggestions are very good, it makes sense to group Penumbra/Til Death Do Us Part/Strange Bedfellows as a 3-parter (and I didn't know that about the episode titles), and then the next three, too - although that might change the top 10 significantly: for instance, I'd rate Tacking Into the Wind much higher on its own than grouped with the other two, because, if I remember correctly, it has none of the cheesy Pah-wraiths stuff.
Thing is though, "The Changing Face of Evil" made it into the last five from DS9 S7 in the Heal/Hurt Game (final, top five from each season). It's the only episode from that not on your list in any form.
The four eps that made it in, but you listed only as possibles are "Progress" (S1), Crossover (S2 - and this one HAS to go in anyway, since the Mirror eps are one of the best-known aspects of DS9, and this is probably the best of them), The Adversary (S3) and Visionary (also S3). Arix's list further cuts Necessary Evil (S2) and Defiant (S3) from the H/H list.
Personally, I'd also include Civil Defence, Crossfire, The Ascent, and Business as Usual on your list. I'll probably end up with further thoughts later.