I think the underlined number it has to do with the time of release, or perhaps the machine that is doing the build. Anyway, I ignore those directories.
You want to work on the Branch builds (aka AVIARY) for now, which is what will become 1.0. The trunk is what is preparing for 1.1, but most of the fun is happening on the branch for now.
Index of /pub/mozilla.org/firefox/nightly/latest-0.9 will always get you the latest nightly build for each platform.
I highly recommend reading the threads by Peter(6) in the
Firefox Builds forum. He has a list of all the fixes put in for that nightly build, as well as a list of significant regressions and/or longstanding bugs. There's also an RSS feed, referred to in the ifrst post for each build.