Dimarzio Evolution pickups - He's moved on now, but these are the classic Steve Vai pickups of choice. I didn't want this guitar to be a clone of his 777 model, but these pickups were fairly obvious for this guitar just because of the association between the respective brands. They are naturally a 4-conductor, making several of the following mods possible. Other 4-conductor pickups would work as well, of course.
Control: Mini-toggles between the vol and tone knobs. They require On/On/On DPDT switches.
Function: This is the real magic of this design. There is one of these for each of the two humbuckers. Each of these switches lets you indepedently get an interesting sound out of the humbucker. Normally I wouldn't use mini-toggle switches, but unlike most other mods, this is one where you absolutely need to use an On/On/On switch, and a push-pull pot only gives you two positions to work with. The absence of a third pot here (compared with a traditional Strat) also creates an opportunity for an intuitive placement of these switches between them, and it's especially easy in a top-routed guitar like most of the RG/Jem models out there since you don't have to do any routing or even drilling other than through the pickguard (which is easy to replace if you change your mind at some point).
Control: Push-pull switch under the tone pot. If possible, I put phase switches in the "extreme" position because it's an extreme sound (though I usually put in on the middle knob on Strats because it affects the middle pickup; there's just no "middle" position here unless I put another switch between the two mini-toggles).
Function: Having a phase switch on the middle pickup is especially convenient on this guitar because it is so un-complicated. Being a single-coil, there isn't much else to do with the middle pickup except reverse the phase. From there, it can be combined with either other pickup (or both even; see below), and there are so many other combinations available there anyway.
Control: Push-pull switch under the volume pot.
Function: Originally I always did add-in switches (as in the link above) so they only added one pickup. However, a DPDT makes it easy to add two at the same time, which actually makes this system a whole lot more intuitive. This "simultaneous add-in switch" adds the both the neck and bridge pickups into whatever is already selected via the 5-way switch. The result is that you can get Neck + Bridge combinations or all three pickups.
Stock 5-way switch options:
2) Neck + Middle
4) Middle + Bridge
With the add-in switch:
1) Neck + Bridge
2) Neck + Middle + Bridge
3) Neck + Middle + Bridge
4) Neck + Middle + Bridge
5) Neck + Bridge
The first and last positions are just the "outside" pickups, and the middle three positions are all the pickups. Pretty easy to keep straight.
The great thing here is that this works very brilliantly in conjuction with the coil taps to give you the "Tele sound" of two single coils at the extremes of the guitar (More technical info about this below). That's great for rockabilly or even '80s pop, depending on the voicing of the pickups you have installed. I've found this really useful and put this mod on several of my guitars since discovering it.
Control: Tone knob
Function: This is something I do on most of my guitars that have a master tone control. I simply change it so that the control only affects only the neck pickup. The reason is simply that I never use the tone control with my bridge pickup (or middle, for that matter). Having it only on the neck pickup means that I can leave it turned down when I switch to the bridge pickup and back again.
The result of all these mods is a total of 46 coil combinations. That's nine times what the guitar started out with! It's a pretty high number, but they're actually really easy to understand and to get at what you need without fiddling around with a lot of switches.
N, M, and B = Neck, Middle, and Bridge, respectively
(s) = series
(t) = tapped
(p) = parallel
(-) = out-of-phase
Pairs of pickups
Total = 46 combinations
The series/tapped/parallel switches are potentially the most confusing, so let me clarify. As pictured, the "up" position is the series configuration; the "down" is parallel. In the middle position the "top left" and "bottom right" would each be connected to their respective common (i.e., middle) lugs.
For the "add-in" switch, the "up" postition adds the neck and bridge pickups to whatever the 5-way selector already has active. The "down" postition is default/stock.
As pictured, the middle pickup as the "hot" lead coming from the left side and the ground on the right.
As I have it drawn, the "tapped" positions leave the neck-most coil active (i.e., the bridge-most coil is cut) for both the neck and bridge pickups. Whether that is ideal for you depends on what you have installed as your bridge pickup. In other words, you need to check the polarity of your middle pickup to see if this gives you a hum-cancelling combination. However, this is somewhat a matter of taste since you can also get the neck+bridge combination (with or without the middle pickup), so maybe you just want a Tele sound (as mentioned above) of two hum-cancelling single coils in parallel (Personal note: I happen to really like this sound), in which you'd really be better off with the neck-most coil of the neck pickup and the bridge-most coil of the bridge pickup.
On the humbuckers, I drew it so that the "hot" lead comes out the top left of the pickup. The one below that (i.e., bottom left) is the ground lead. The two on the right side are the leads that would normally connect in series.
The red circle on the tone knob is the capacitor, of course.