I just thought I'd post my own experience with the ol' RS3000. Maybe it will help some others trying to determine whether or not they potentially have a keyless system installed.
I have a 1997 T4R that I purchased 7 years ago. It came with no keyless remotes, but I had always noticed the security light in the console area right by the back window button. Just recently, after reading various threads on the forums, I decided to call up the local Toyota dealership and had them look up my VIN. Their answer was "most likely no dealer keyless system was installed". I then called up the dealership I originally purchased the vehicle from. They, too, said "it does not appear a keyless remote system was installed", even after I mentioned the RS3000 box under my driver's seat and the piezo chirper in the engine bay.
After pushing the little green button on the side of the RS3000 unit and seeing the security light turn on, I figured to go ahead and try out a remote (two button black), which I ordered from replacemyremote.com.
When I got the remote, I tried pairing it and, though it did seem to cause something to happen with the lights and horn briefly, the vehicle wouldn't respond to any subsequent button presses. I decided to "clear all remotes" from the ECU and then proceeded to redo the pairing--HUZZAH! Now I had a two button remote that could unlock and lock all doors, but only with the top button.
Here's where it gets a little weird (and might be useful to others)...
My remote has two buttons, but the bottom button seems to serve no purpose. I contacted the company I purchased the remote from about this and they suggested I swap it out for a replacement. As I was about to mail the package, I noticed the address was about 30 minutes away, so after emailing with them, I decided to drive down in person. Turns out, this was a good idea. They gave me a second remote to try, but I was unable to get any response from my 4Runner with it. As I waited for them to get me a third remote to try, I was googling about the RS3000 system and ran across a site that suggested only the top button on the remote is supposed to work. The third remote they gave failed to elicit any response from my 4Runner as well. They offered a refund, but I decided I was happy just to have a working remote, so they gave me the original back and it paired with no problem.
So now I have a remote. Apparently it sets a alarm that I never knew I had. When your vehicle is locked via the remote, it must be unlocked via the remote or else the alarm will go off. I'd rather just turn the whole alarm function off, but the Valet mode setting does not seem to hold for very long (my wife learned this early one morning). I need to dig up an old thread where someone says he just cut the wires that cause the alarm to trigger and make that modification. (EDIT:
found it) Additional EDIT: Made this wire-cut modification and had no luck. Alarm will still go off if the 4Runner is locked with the remote and unlocked with the key. Also, as mentioned in subsequent posts by others, my chirper goes through strange periods of sounding normal, not sounding at all, sounding like it's dying, etc. Also, the 4Runner does not always respond to the button press. Sometimes it takes a few mashes before anything happens.
The moral of the story is that regardless of what the dealership says, and even if a remote doesn't seem to work for you initially, you might still have keyless remote potential. If the components are there (chiefly, the RS3000), you should be set. And if one remote doesn't work, another might.