Some more initial thoughts about organizations, subject to change.

Gaining and Losing Rank
Any organization should have definite aims and goals, and the most obvious way for a PC to gain rank with respect to that organization is to further its plans.

An organization may offer the PC missions and quests. If a PC completes them successfully, he may gain rank with the organization in addition to whatever other physical rewards (gold and magic items) it offers.

Even if the PC does not work directly for the organization, his accomplishments may help or hinder it, resulting in a corresponding increase or decrease in rank.

Both of the approaches above require some preparation from the DM - either to devise tasks which the organization wants accomplished, or to determine the organization's reaction to the PC's deeds (assuming it comes to know of them).

Alternatively, and perhaps ideally, the PC may take the initiative and come up with his own plans to increase his standing with the organization. The DM could run this as an impromptu complexity 1 (4 successes before 3 failures) skill challenge of a level equal to his current rank +6. The details of the skill challenge will depend on the organization and how the PC chooses to advance himself. If the PC succeeds on the skill challenge, he earns XP for the skill challenge, a one-point increase in rank, and the organization may reward him further, at the DM's discretion.