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.

Same reason why I took out Defiant at Arix's suggestion - it is OK but for some reason it's not on my "best DS9 episodes" list, despite everything that it has going on for it (Tom Riker, The Maquis, Dukat working with Sisko, The Obsidian Order, the Defiant itself...). I guess some episodes have that extra something and some are just the sum of their parts. (Frankly, I feel the same about The Way of the Warrior, but so many people are crazy about it.)
See the other posts in this thread for the reasons why I included 
some people listed episodes like Progress, Blood Oath, Take me Out to the Holosuite etc. that I haven't included in the list above