Now this is stricly a theoretical matter for me now, but if I'd still be playing D2, I'd still be clearing lots and lots of alvl85 areas for items and occasionally finding a rune or dozen along the way. If I'd get enough runes to create an runeword item I'd like, I'd make it. If I'd have to cube some runes to do so, I'd cube them.
When I did my runs, I didn't bother with just one specific area, such as Pindle, I did alot larger scale running. Each game I started out by clearing everyone's favorite: The Pits. After that I tried my luck with the slot machine Countess, who never dropped a single good item/rune, think the best was some mid lvl rune such as Hel. After she croaked I continued to kill my favorite: Andariel. It's just amazing how much items you can get from her in a very small time. This is also a place where a random Zombie minion dropped me a Ber rune while I was doing my 1000 Andy run listings.
After that it's normally time for me to head into the 3rd act and kill Mephisto, who has never been too kind for me in drops. When that's done and over with, I continue to Shenk & Eldritch who both drop some relatively useful items occasionally, and are fast to kill aswell. After that it's Baal and it's minions.
Now comes the most important part of my runs, while it doesn't give out much items normally, it's the best for the runes...Act4 River of Flame & Chaos Sanctuary. As the Wraith class monsters have increased chance of runedrops and they're both alvl85 areas where you encounter them, it's just natural that those are the good places. And that's not all, there's Hephasto and the super uniques at the Seals along with Diablo himself. What more can you ask?
Still, the best rune I've found was the Zod from some minion of Baal, don't have any idea which one as I had killed them all before clearing...ah well, you know the story (I've posted it so many times already). As for my second Zod, it's cubed from a Cham and other high level runes I traded from a reliable source (My own brother), along with couple runes I had found myself of course.
Just keep playing and you'll get the runes, it might take years or then it might take couple of hours, it's all a matter of luck. Still, you don't need BotD for anything, nor do you need Enigma, or CoH. Infact, the game only becomes more boring since a huge portion of the challenge is gone after you get the best items (talking about game difficulty, and the challenge of getting your personal goals).