Is there a complete D&D 3.5/Pathfinder mass combat rules set for conducting siege warfare, or do you have to cobble together incomplete rules from different sources (Stronghold Builder's Guidebook for siege weapons + Pathfinder Ultimate Campaign mass combat rules)?
If you feel up to adapting a system from an earlier edition, BECMI D&D had the War Machine rules for mass combat, and the Siege Machine extension to those rules for siege warfare, both available in the Rules Cyclopedia (available in PDF from dndclassics.com.)
It ought to be fairly simple to adapt as it's based mostly on things such as average hit dice and AC of troops, so you just need to make an adjustment for the inverted AC of that edition of the game.
Note that War Machine works at the unit/regiment level - imagine a map, with each unit (which could be hundreds or even thousands of troops) represented by a counter with it's own statistics, making it comparable to most historic battle diagrams (1st archers, 2nd archers, 1st Mounted Knights, and so forth), and is designed for play on a hex map of the area (although you could feasibly use a square grid, too.)
Heroes of Battle and Ultimate Combat discuss mass combat primarily from the perspective of the battlefield as a setting for an adventurer party. Several campaigns and adventures, like the aforementioned Red Hand of Doom, also discuss mass combat going on around the players.
But you will never find a true rule system for army vs. army in 3.x, because rule systems for such events form an entire genre separate from roleplaying. Wargaming is a big hobby, and while Dungeons and Dragon has its roots in wargaming, there has been a lot of divergence. It would be crazy for an RPG developer to try to shoehorn an entire wargame into their system, and I doubt anyone has tried.1 I’m going to quote wholesale from Heroes of Battle here, from Think Big/Play Small section on page 6.
By their very nature, wars are large affairs. Not even counting support personnel behind the lines who supply food and munitions, or medical personnel who care for the wounded after a conflict, a single battle can involve hundreds if not thousands or even tens of thousands of soldiers.
That’s not roleplaying. That’s wargaming.
Think about those great war movies. They’re not about huge battles fought for geopolitical ideologies. They’re stories about small groups of well-trained people going on dangerous missions. They might have been ordered to go, but each person in the group usually has his or her reasons for taking the mission, whether it’s for greed or glory, advancement or adventure.
Now, that’s roleplaying at its finest.
The trick to turning the battlefield into a dungeon is to think big, but play small.
In short, if you’re worried about the details of the makeup, disposition, and supplies of each force, you’re playing a wargame rather than an RPG. Which is perfectly acceptable, but Dungeons & Dragons isn’t the place to look for rules on playing a wargame.
So really, if you’re serious about having a system in place for determining the results of the siege and playing that out from an army level, you need to start looking into wargames.
1 Some companies do make both wargames and RPGs for the same setting, of course, Warhammer being the big one. However, in those cases, they are specifically different product, by different teams, and one is not “inside” the other to the best of my knowledge.
The 3.5 campaign book Red Hand of Doom includes rather lengthy discussions on how to conduct a siege, how to handle a massive army moving cross-country, and how to handle groups of NPCs helping the players fight the horde off at different stages. Also gives figures for various advanced scouts, roadblocks, and other factors off moving large armies.
Unfortunately does not give anything for having two armies clash on an open field of battle, but that was never the point of the campaign.