One of the things I notice in most games I play in (and sometimes the ones I run) is that sometimes there'll be a thieves guild (usually to antagonize the PCs), a church (for the divine PCs to have meaningful interactions, provide restorative spells), often times a mage's guild (for the arcane PCs to have meaningful interactions, copy spells from). But it's hard to write in some sort of martial guild.
You can put in a mercenary group, but the PCs usually aren't looking to hire, they're the heroes of the story after all.
So what kind of organization would you like to encounter when you're playing a martial character (or have enjoyed encountering in games)? What quests could this guild/dojo offer?
What if you could broaden your skill at this organization, like Wizards can copy spells, a character with all martial weapons could spend some time (and gold) to learn an exotic weapon, or expand Weapon Focus to another weapon?
Some of the prestige classes require memberships in organized martial groups. If you're looking for mechanical aspects I'd start with them.