I've recently been playing Fallout 2 and was hoping for some help in regards to the best order of town/cities. I mean what is the most effecient order to playing them?
Well, the "usual" (and loose) order is Arroyo, Klamath, the Den, Modoc, Vault City, and Gecko, then (roughly) on to Redding, New Reno, Broken Hills, New California Republic, and finally San Francisco, with Navarro, SAD, the Military Base, and Raiders sprinkled anywhere during the middle to late game. You'll be returning to New Reno, Vault City, and NCR a lot, as well as (to a lesser degree) Gecko and the Den.
Again though, this is very loose.
Also, if you does it matter if you return to arroyo with the geck after the sickly & desperate vision from the witch doctor, or is it better to return earlier?
I can't remember. I don't think it matters, but it might (for the ending Arroyo gets once you beat the game).
Finally , is there any time limit to rescuing the arroyo villagers after they've been captured?
Nope, just the usual hard-coded limit of 13 total game years.