I used mine all the time in R/S/E just as a place to hide and relax and pull out the interior decorator in me. That was a lot of fun, even for a short time. I still do it when I play and like to get the best base possible.
In D/P, I never used it because I would have had to go underground and turn on my communications (thus draining the battery), plus those stupid rocks were everywhere and it made it hard to decorate. They basically killed the charm it had. And coming into this thread, I completely forgot about the existence of Secret Bases in D/P/P... :-X