Q: external hard drive, os limitations

Is the operating system limitation only for using the software that comes with the hard drive, and not necessary for simple usage of the hard drive?

Probably for the software, so you won't have problems with it

If I buy an external drive that isn't specifically made for macs, are there certain drives that won't work with a mac system but only a pc?

They should work because you only have to format it in Mac OS Extended or FAT to use it in a Mac

also I'm just now assuming that I won't be able to find an external hard drive with firewire, unless it's been specifically made for macs?

They are made for Mac, but they can be used in non-Macs if they have got another port (USB)

Go to OWC and check out their offerings. I have an external OWC FW drive that I use with my G4 Powerbook for back up with FW startup ability.

http://eshop.macsales.com/shop/firewire/on-the-go

The 'for Mac'/'for PC' designation really has to do with any bundled software and/or pre-formatting used on the drive.  You don't need the bundled software and the formatting is easily changed with Disk Utility to meet your needs.

It must be Firewire to boot your PPC Mac.

I don't have a current list but some drives in the past that 'should' have worked have not worked when it came to booting Macs.  They were okay once the computer was booted but the chips used on the enclosures didn't have sufficient support at the boot stage to conduct booting.  The manufacturer wasn't always aware of this or didn't care since most of their sales were for PCs

With external drives you have two components. You have the enclosure and you have the drive, and both have to work in concert.  I prefer buying an enclosure I know will boot my Mac, and a drive I know to be of quality I trust.  Although I don't like pushing particular companies, the OWC/Mac-sales.com mentioned elsewhere has the edge in that they specifically deal with Macs so you can be pretty well guaranteed anything you buy will play nicely.  I would at least get an enclosure from them.  Their hard drive prices are pretty much in line with market rates (maybe $10 higher but by the time you ship from another vendor it will cost that much extra).

I haven't been following hard drive ratings too much recently. Seagate used to be tops 10 years ago (I still have a dew in my computer I bought back then), then became the pits 3 years ago.  Western Digital I used to rate so-so but last I looked were the best although they do have several levels of drive (green, blue, black, enterprise) with different ratings.  Hitachi may be making a comeback too, though in the end I am not sure who is really owned by whom and if they are really different.  I usually check places such as Newegg which has many, many reviews and see what people say there.  Realize a few people will always end up with duds.  See if you can find ratings related to longevity and things you find important such as noise, speed, etc.

For regular booting you want a fast drive (7200 rpm +).  For periodic booting you can tolerate a slower drive.  5400 rpm drives will be cheaper and probably cooler.  "Green" drives are often slower.

If this is purely for storage and rare booting, maybe look at getting multiple drives (backup always!) and one of the Newertech Voyageur docking stands.  These don't have any active cooling and mine does run about 100°F so I am not sure if it is what you want for running 24/7.