I'm sure all high quality guides of each of those will explain how an army of Hydras murder-screw everything in D&D.
This is possibly the best thing I have read this week. Thank you.
So, anyway, on to the discussion at hand:
I can say that I have had the fun of playing a Bone Knight character from level 1-20. We did not have the most optimized group (Summoner Sorcerer, Rogue SA Pouncer/Martial Adepts, and a Dervish/Warblade), but I was hands down the most powerful one even with 2 CL down. What you have to remember is that Cleric is one of the BIG 5 classes. The best of the best. So unless you find something that is just Cleric+, like Planar Shepherd is to the Druid, you will always be sacrificing something. As a random side note, I think that is supposed to be the point of a PrC, anyway, to move your focus into one area.
So, what I did was Human Paragon 3/Cleric 1/Church Inquisitor 6/Bone Knight 10. Not in that order, I took Bone Knight at ECL 7 with partial BAB. This lost me 2 CLs, but most of the Clerics best spells come at the 3-5 range anyway (ignoring Gate, Miracle, etc). I had a 32 point buy that gave me something like STR 14/DEX 8/CON 12/INT 12/WIS 16/CHA 15 using the middle age template. Human Paragon raised Wis.
I focused on buffing the party and using no-save debuffs on the enemy, along with some intimidation with Imperious Command/Never Outnumbered. I also used Divine Defiance and various CL boosters to counter/dispel enemy casters while DMM: Quickening buffs. I crafted armor and weapons, so my AC was in the mid-high 70s by level 20 and my mount was generously equipped, as well. My own equipment used the standard mounted charge items to get all the feats without spending feats.
In the mid levels, after I got my Fill the Ranks and Bone March I stated amassing utility undead (yeah, combat isn't everything). I used the Karnathi undead to pilot a ship (who has the resources for Profession: sailing, anyway?) and I had a group of Ankheg that I used to tunnel, excavate, and generally reshape the terrain to my whims. Eventually I acquired a Purple Worm zombie to act as a bit of siege equipment (although that was part of my normal turning pool). Undead armies are useful for more than just combat.