The tone pots are fairly useless, for the most part, so I was wondering what else people have done to take advantage of having those two controls available. I would love some ideas of something I could put into the electronics of my Strat and hook it up to one of the tone pots....
Tone pots are absolutely not useless. I used to think the same because I never used them, then I plugged my telecaster set to the bridge pickup into a new Vox AC-30 and experienced a shrill piercing nasty noise that somewhat resembled my favorite axe. Tone pots to the rescue!
Albeit subtle, the effect you get from your guitars tone potentiometer is useful in a couple of applications. Some of the more subdued tones you hear on popular recordings--and very much most of jazz--utilize the tone being kicked a couple of notches down. It's specifically nice for taking the edge off those harsh tones that exist on overly bright amplifiers (like a Vox) in combination with a bridge pickup.
As for what you could do as a replacement: the sky is the limit. For a Strat you could consider the following ideas:
Blend Pot: Some higher end G&L's have these, and I enjoyed it thoroughly when I owned a Legacy HB. The basic idea is you wire up a potentiometer to blend a target pickup into your overall tone, or pan between two target pickups. This would open up some tonal possibilities not usually available to Strat players--but how musically usable those tones are is up to you. You can find some wiring diagrams and more information on the basic idea here. These tend to be more useful for the so called "Fat Strat" configurations because it allows you to blend the humbucker into the single coil sounds for some more balls.
Mid Boost: Eric Clapton used something similar to this on his black Strat I believe. You can pick up a kit here. This is a bit advanced, and you'll need to install a small preamp underneath your pick guard along with a battery to run it. I've never installed one of these, so YMMV.
Individual Pickup Volumes: This is one of my favorite mods. If you've ever used a Les Paul then you understand why the stock wiring of multiple volume pots can be slightly irritating. When you kill one volume entirely the whole guitar goes dark at the middle switch position (or bridge + neck). This would be a way to independently control the output volume of each pickup instead of having a single, master volume. Using this wiring we would still have output at each switch position even if one of the involved pickup's volume is at zero. Take a look at the following diagrams:
The right diagram is a variation on the volume pot wiring that will get you the ability to control each volume individually instead of having a single, master volume. The picture to the left is the standard way of wiring a volume pot, and the picture to the right is sometimes called "reverse" wiring. Sources for those diagrams along with some other great free information is located here. By wiring up all your volume potentiometers this way you are able to independently control the volume of each pickup without effecting the master volume of the guitar. This is great because it in effect gives you more options than a single blend pot at the expense of using up another potentiometer for each pickup whose volume you wish to control. So by swapping out your tone controls for unique pickup volume controls, you are able to keep the basic sounds of each of the five switch positions but blend the volumes of each pickup included in the tone the way you would be able to on a Les Paul. There are many other benefits and drawbacks of this mod, but I think you get the general idea.
Anywho, there are tons of other weird and nonstandard modifications that you could take advantage of out there. A quick search for "stratocaster wiring diagrams" should turn up a plethora of hits. Deaf Eddie also has a great site on Stratocaster wiring mods and can give you all kinds of ideas (I learned a lot from him). Check him out here.
With one of the early guitars I built, I used the 2nd tone selector (for the neck pickup - so I never used it) as the input to a small wah wah I built into the body. I could hook my little finger around it and use it as a fairly extreme tone selector or as a full on wah.
I replaced one of the two tone pots in my Strat with a five-position rotary pickup-selector switch (I then re-wired the second tone pot to be a master tone control for the whole guitar). In combination with the stock five-way selector, the rotary switch allows for pickup combinations that the five-way selector by itself doesn't allow, such as Tele-style outside and inside pickups, in-phase or out-of-phase combinations, serial or parallel wiring, coil-tapping the bridge humbucker, etc.
On the guitar I built from Warmoth parts, I have piezo pickups embedded in the bridge saddles, and I use the middle pot as a magnetic/piezo balance knob, again with the third pot as master tone. I also added a three-way mini-toggle for magnetic-only/magnetic-and-piezo/piezo-only options.
Above I posted a link to the g&l Guitars wiring diagrams page. Check the Legacy model -- 3 single-coil pickups. They use a True Bass and separate True Treble pots.... Like a home stereo used to be....THE GREATEST.\ you can actually cut or boost the bass !!! likewise for treble. imagine a true boost in the bass...not just a rolloff of treble...
AMAZING Tone Switches. 3-wire simple installation. THIS IS THE COOLEST MOD I'VE SEEN..AND USE.
I actually removed mine on my ESP and replaced it with an EMG PA2 preamp booster. It's nice because you don't have to drill into your body, and reverting is quite painless if you don't like it.
ModBoards from Guitar Fetish will allow you to have chorus, wah, tremolo, compression, delay or distortion in that knob space. What I've heard about them hasn't been 100% favorable, but they're options.
You could mount another type of pot, push-pull switched one or a switched one (like in an old radio), or a pushbutton in that hole. A button as a killswitch (see Buckethead, Tom Morello) is a common option.
A simple switch is probably the easiest replacement. Simplest thing to use it for is probably a coil split or other such mod. One thing I've done is take a guitar with HSH pickups, wire the five position switch to the humbuckers (various combinations, you can find many kinds of schematics) and have a spare switch add the middle pickup. It could also switch between the HBs and the middle pickup if that's a more useful combination.
If you go active, there's loads of things you can use the hole for. :)
I had my tone pot turned into a spin-a-split. This gives you control over how much you split the humbucker, from both coils full to fully split. I don't like how the pickup sounds in either of the extremes, so having this control is very useful.