I don't know any of the engineering physics behind the spring-under vs. spring-over debate, but like the others said, I've heard that spring-under helps prevent axle wrap. I also heard that spring under actually allows more flex than spring-over; hence, the reason why so many desert racing setups go with a spring-under configuration. But I don't really know if that's true or not, and CUBuff 4Runner's post tends to dispute that, so it's quite possible that I either heard wrong or that I misunderstood. My only experience with spring-under is that my old 1947 CJ2A Willys is spring-under and actually works alot better than the spring-over modification that one of its previous owners did to it, but I don't know if that's because the stock springs were used (which were designed for spring-under use to begin with) or if the little CJ2A platform is just not suitable for a spring-over configuration to begin with.
I do know, as I'm sure you do as well, that rockcrawlers go with spring-over not only to gain more lift for bigger tires, but to also have less things to get hung up on the rocks. But since you have a Prerunner, I doubt you'll be trying any rockcrawling. So that may not be as much of an issue, unless the type of off-roading you like to do includes trails with minor rocks, tree roots or other obstacles which could still be a potential source of things that can hit the lower-hanging components of a spring-under configuration.
the dezert guys arnt going spring under for the flex, more like travel... a spring will only go so far regardless of whether its above or below the axle. the dezert guys are spring under to get a longer leaf pack (like the 62" deavers) with more arch without lifting the ass-end in the air like a spring over pack will do. more wheel travel minus the lift.
CentralCoastTaco99 is right about the travel a spring will only go so far over or under. I was thinking more about the front where you can run into more limiting factors that will reduce the travel that you can get out of the same spring. For example if I were to have my springs flat in the front with spring under I would be hitting my oil pan. Not saying it is impossible, just the majority of spring unders I have seen rockcrawling don't seem to have the travel.
I've just done SOA conversion on a 1987 suzuki samuria and welded some special upper spring perches on..With those perches I should get about 6" and I think I'm also going to re-arch the leafs while I've got them out... It sits alot higher not I've not drove it yet but should think it'll flex more.. I'll hollla at you once I get the perches miged back on and everything bolted back up..