I had driven to the store a few weeks ago, and after running in to load up on beer, my 4Runner started, but the idle began to drop until it died completely. Now it won't start at all. My first thought was that I ran out of gas (I was really low but can usually eke out enough extra miles to keep going), but put in about 3 gallons and still nothing.

I went off-roading/mudding a few weeks before this happened, and ever since my starter sounds a bit rough when cranking, but it still cranked and once the engine was running, it ran just like it always had. The starter cranks a little weakly right now, but the fact that it originally died after it was running makes me think it's not the starter.

I've replaced the fuel filter & I hear the fuel pump run. (So it's probably not fuel)

I've cleaned my entire intake assembly including the throttle body and IAC valve, and that hasn't worked. I'm about to get to the spark plugs, but just wondering what's the best way to test them and/or the wires/coil packs? The way I've heard/read about is just resting the plug against some part of the engine block and looking for existence/color of the spark. Is that it?

Check all the basics spark, proper fuel pressure, check for codes and watch live data while cranking if you have a good scanner.

Is there a way to check fuel pressure without a scanner?

A scanner wont give you fuel pressure data on the 4runner. You need a fuel pressure tester/gauge. The scanner is to watch live data needed to the egine to start and run things like cam and crank signal, fuel pump requested on ect. Most people dont have this equipment or knowledge. If you dont know how to go about checking the basics your are best taking it to a good repair shop.

i have chased an issue similar to this for a while myself. for me it would sometimes start, sometimes not, it would crank hard so i knew i had good electrical power to the starter and it wasnt the battery(something you might want too look into by the weak/labored cranking you describe). i thought it was a fuel issue, i could not hear the fuel pump -so i replaced it. didnt fix the issue, and still cant hear the pump. so then i went to the pump relay, nope not that either... for me it ended up being the EFI relay -same relay part number though. one way to trouble shoot this as the scenario is to pop the hood, pull the cover on the fuse box under the hood and swap the EFI relay with the tail light relay -also the same relay part number. then try to start it. if it starts right up then you have a relay and its not allowing the EFI/injectors to pump fuel into the cylinders.
i dont think its your spark plugs or coil packs. those typically give long warnings before they go bad, like misfires, rough idle, rough running, cutting out ect. they are not a boom done type of deal.
the other thing id look into is your battery cables, and grounds. is your battery tied down with the factory bracket, or do you have a bungie-cord holding it place? if the battery is not positively secured and can move around it can yank wire/cables and cause labored starts ect. get a volt meter out and check the batteries level. pull the leads off the terminals and hit the battery terminals and wire leads with a wire brush/terminal cleaner and put things back together and try it. also check the main ground going to the side of the block next to the oil filter. a simple break in the electrical circuit will stop a vehicle dead in its tracks, and a poor or bad connection will quickly drain and kill a battery. also you might want to check the alternator -no alternator likes mud or contaminates.

good luck

I was going to say possibly relay or fuel pump on the way out

Check to make sure you are getting fire and fuel. Could be a cam shaft position sensore or crank shaft position sensor. Or hook up a scanner and see if your vehicle registers RPM's

something like this, running car died and never started again, happened to me before and it was the timing belt had broken. I decided to scrap the car. It wasn't a 4runner.

Good luck.