On of my favorite tools I never get enough time to use is expect. What is expect? Expect is a scripting language that let's you automate responses to scripts or daemons and pretend to be a users. So you can write a script to say update the passwords on all your systems with just one command. Another way I am planning to use this in the very near future is to do MD5 Check Sums on a file and compare them. If the files aren't then it will the re-copy over the files that are missing. Over at linux-mag.com they have a great gettings started document you should check out to see if it can make your life easier.
I came across an article over on the Gaurdian talking about the real lack of need to the larger more established solutions. When you start developing on Linux or FreeBSD the points in the article ring even clearer. Even if you are developing Java applications whether you should use the free eclipse solution or a packaged eclipse solution like IBM's RSA or RAD or the much cheaper MyEclipse's cheaper but still costing solution. If you want to save your company money take just a little bit of time and something to develop and look at the many free and open source options available.
If the application you are having problems with does a lot of reading and writing to files a quick fix might be to use a RAM based file system. Yes that precious RAM we all love to have for our apps might be better spent creating a temporary file system. If you then copy the often written to application files onto this RAM based file system you should see tremendous performance increases. With systems running the Core i7 architecture the boost could be even higher because of the higher RAM speeds and lower latency between the CPU and the chips. The only way to find out though is to give it a try. To do that you will need a RAM Disk of some kind. I found this how to over at Linux Mag that should be a good starting point. While I haven't done these exact instructions, I have done this before and they seem to be correct. As with anything though your mileage may very. Test your solution thoroughly before implementing this in a production environment. Remember you are dealing with RAM and if you have to reboot anything not saved off from that RAM Disk will be lost.