A broad field you meditate on. I don't know much about Linux distributions - I do my development (at home) on a Win2k box, at work I use Solaris and Windows NT. I can offer three answers to your questions :

First, plan to throw away everything you'll write in your first two generations. In my experience, you need to have implemented a task at least three times, before you know what the important details are, and what approach will work in the end. Don't invest in a large scale object model or too detailed planning, as it will tie you to the bad ideas you had at the start. You maybe already have gathered some experience in your field with your one-off scripts, but that experience won't reach far enough for a help-desk application. In my opinion, you should first write all the one-off scripts as separate scripts, and watch out what parts can be abstracted into modules, and what parts simply aren't worth the bother. Remember that when you change a module, every program that uses it needs retesting, but when you change a copy of the module, only the program you're working on needs retesting.

From my experience, you can't have enough logging. Period. Rotate the logfiles daily, if diskspace should be of any concern, but log everything. Don't make it configurable or somebody will switch it off. Logs aren't there for when everything works as planned, but they are there for you to stare at after something unexpected happened. Plan for an easy parseable format, and for logfile viewers (CGI maybe) that allow you to specify different levels. But don't throw away the log data.

From what you describe, you'll be working alone - this is a bad idea. You need someone to discuss your thoughts with, and your boss will also need somebody to take your place when the bus runs you over. A lot of bad design ideas get killed by explaining them to somebody else.

perl -MHTTP::Daemon -MHTTP::Response -MLWP::Simple -e ' ;    # The  
$d = new HTTP::Daemon and fork and getprint $d->url and exit;#spider
($c = $d->accept())->get_request(); $c->send_response( new   #in the
HTTP::Response(200,$_,$_,qq(Just another Perl hacker\n))); ' #  web
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