Yeah, easiest way of fixing this with the RS3000 system is to get a new remote from mykeylessentry on ebay. I got one and it works great. It doesn't look as "stylish" as the original but at least it can withstand a drop, and it's only $15.
I drilled a fishline sized hole through the keyfob and then went to a jewelers shop. Bought a thin lined key chain attachment that has worked ever since.
If your fob is the style jij posted above (my 2002's is) you can get a replacement case from Autozone made by Dorman.
They don't make one for the 4Runner (that I can find on their website - www.MyKeylessRemote.com) but they do make one for a 2002-2006 Camry that is identical except for the small inner ridge on the bottom of the fob. Part # 13614, it's $15.
You will need to Dremel away the ridge on the inside back cover where the battery holder is attached to the circuit board (it will be obvious to you once you put the circuit board in the new back cover) but that only takes about 5 seconds.
They even had the button battery (CR 2016) so in 3 minutes I was all set with a brand new fob.
I got this tip from Mountain in another thread but tought I'd post here as so many are asking.
I just got mine in and they were a direct swap over, no modding needed. They look almost identical to the factory one and were $13 for a pair. Swap over was less than 30 seconds and they work great.
FYI, I just released the 4 button remote case with titanium for the keyring and a nice band up the sides. This is the longest lasting remote case you'll ever see for these remotes!