Reputation and networking was one of the first things that caught my eye when I first picked up Eclipse Phase. In 1st edition they seemed somewhat disjointed. Transhuman changed some of this by combining the two into one mechanic. This was better but something kept tugging at my mind. I've always imagined networking as how broadly the character was recognized among certain factions and reputation as the opinion that network had of the character. Just because someone is well know does not make them well liked. Just because someone is well liked does not make them well known. The combined networking/rep didn't feel like it fit this model well.
To this I wrote a hybrid form of reputation and networking for my home group. I divided rep into two groups, total and disposable. The total rep is like a swimming pool and the disposable rep like the water inside it. The disposable rep would ebb and flow but not beyond the bounds of total rep. Total rep replaced networking in a since. This is the value that the players roll against to make tests based on their networks. Disposable rep was treated almost like a currency and fluctuated as the players called in favors for their characters. After a mission was over they could use downtime to restore disposable rep but only up to the same level as their total rep.
Total rep also determined the number of NPC contacts each character had in a given network. The players would write out their contacts on flash cards and loved making background stories for them. When a player called in a favor their character needed to communicate with the NPC they felt best provided for their particular need. I feel it still needs work but the results so far have been good.
Have you you used reputation and networking in the past? What has worked best for you?