The major bane when I update Ubuntu (which is way more frequent than Windows) is that I lose all installed application. To be precise I do a lot of Maple, Matlab, Geogebra & for all of those I install Java platform which too isnt very straightforward plus the license management things, which really give me craps. I don't install application in /home (to be made available to all users) thus a separate /home partition is meaningless. Can we circumvent this problem somehow such that Java dependent applications along with JDK doesn't blow away after update, may be by a separate partition (just like /home) where only custom (other than provided by Ubuntu Software Center) install application resides

Further: I use specific binary of Java (Java6 update 32), its an important requirement for me, thus I don't want to let it crash/overwritten or similar