Is there any type of daily/weekly maintenance that can be done to optimize NLE software, specifically Premiere Pro CS4?
There is software to optimize the windows operating system - Iola Software is one company, but I don't really recommend any of them, so the answer I guess is, "No".
How often do you Defrag? Do you do it even if the analyzer says you don't need it?
Don't believe the analyzer! Defrag every few days, if you've been editing and for sure, defrag everytime you remove an old project (and don't forget to remove the temp files!!)
Are there folders that can be cleared (temp files?) that keep things from getting bogged down?
Yes, check your project preferences and know where your temp files are being stored. I got slack on this once and found temp files from a year back taking up many gigabytes of space.
At what point is a hard drive too full to operate efficiently?
Well, this answer is from my own experience, but I've found it's best to keep a drive from going much over 50% full.
CS4 has its share of issues but how much of them can be avoided or minimized by proper maintenance?
I guess this depends on where you draw the line between "CS4's issues" and "System issues". It's important to keep all drivers up to date and be aware of any compatibility issues. This requires logging into Adobe's support forums and your video card's support section from time to time and it requires checking every week for updates.
Also, at the current price of computers, it pays to have a dedicated video editing system with no other software than your editing, capture, effects software. Office, games, email, etc. should not be on this system - period.
I have been running CS4 pretty smoothly that past several weeks - even After Effects has run for me.