An Argument for The Countess
Mephy, Baal, and Pindle + other A5SUs are commonly referenced in MF guides for 1.09. As discussed above, the CP/GT/AW caves are also very good (in my direct experience). However, another very good MF target is The Countess. She has a significantly higher item generation rate than other SUs, probably due to the fact that she always drops 4 items, and they can potentially all be items (so 4 unique items are possible). Also, her automatic attributes are different than 1.10+ Countess - in 1.09, she always spawns CI/FE, and often spawns Stone Skin/PI (like most unique monsters in the game). She's never LI. As such, a lightning skill will always be effective, and a fire skill will always be somewhat effective.
As mentioned previously, 1.09 Countess has lower drop rates than 1.10+ for runes to Ist, but drops
Gul and
Vex as special rune drops. This is pretty much offset by how much faster 1.09 Countess is to run due to the small maps. However, 1.09 Countess drops SIGNIFICANTLY better that 1.10+ Countess for items. According to ATMA, at 200% MF, 1.09 Hell Countess drops Skin of Vipermagi, Oculus, HoZ, Staftstop, etc. AT LEAST twice as frequently as 1.12 Countess.
Further, NM Countess' TC availability is bugged to be equal to Hell Countess TCs - that means NM Countess can drop up to TC66 (I personally had my first LoH from NM Countess), but since she is only mlvl 44, she can't drop the uniques of higher TC items, but since LoH and Dark Adherent have qlvl of 39, she can actually drop those. She can drop all the handy exceptional Set items like Aldur's Rhythme, Guillaume's Face, IK Gloves/Boots/Belt, Sazabi Helm, etc.
So - The Countess is a very good MF target in 1.09 for exceptional level items and some elites (Wizzy/Shako). I have personally gotten Vamp's Gaze, Arm of King Leoric, Stone of Jordan, Highlord's Wrath, Butcher's Pupil, etc. either from The Countess herself or from the variious champions/uniques on the way.
She is also a better source for twink gear on Normal than 1.10+ (not for good runes though - she only drops El and Eld in 1.09 Normal). For instance, she is the best source other than the Cow King for Death's Gloves and Sash in 1.09.
Finally, the Tower is a great place for racks - I have a Wire Fleece rack on my Druid's map that has provided plenty of runeword bases, a Wyrmhide rack on my Amazon's map, and a Luna rack (that has already produced a Blackoak Shield) that can also be manipulated to drop Monarchs (I have all the 4os Monarchs I could ever want now), AND a Russet Armor rack that has produced Skullder's Ire on my Sorceress' Tower Map. I also discovered a Gilded Shield rack in my Pally's map that is paired with a Highland Blade rack.