My question(s) is (are) : my internal HDD is a 5400rpm S-ATA drive.. can I get an external HDD that's faster than that, or will it cause me some kind of trouble?
Nope. The first HDD I used externally was 7200rpm while the one in my computer was 5400rpm. You're more to be limited by the fact you'll be restricted to USB 2.0 transfer speeds than by the rpm difference between the main and external drive.
If you'd prefer to have the faster drive in the computer itself, just buy a regular 7200rpm internal drive and an external enclosure, clone (or completely reinstall from scratch) your existing system onto the 7200rpm drive and use that as your main drive instead. Then you can slap the 5400rpm drive in the enclosure and use it for storage purposes. Or buy two 7200rpm drives and 2 enclosures and use the 5400rpm drive for non-important storage (the one I mentioned as being in my setup is now used to store my digital music collection, and both my main and editing drives are 7200rpm).
Also, will the computer run slower if the programs I'm using are installed on the internal HDD, but the files I need to process are on the external one?
Generally, you probably won't notice the difference, if any. Like I said before, the transfer speed of USB 2.0 is more important there.
p.s. : I don't have a Mac right now, but I've been thinking about getting one in the future, so I've been reading stuff on the net about it.. As far as I understand, one can only add an external HDD to a Mac if the said HDD is formatted with the Fat32 file system /which limits the file size..
bla bla bla.../ Anyway, my question would be /just for future reference/ : do you guys know any way of going round the whole formatting thing when dealing with a Mac /thus keeping the HDD NTFS/ ?
OS X can sort of handle NTFS, but it gets finicky sometimes (at least as far as Tiger is concerned; hopefully Leopard/Snow Leopard has improved support). There were times that it wouldn't even recognize my NTFS drive when I turned it on. Other times, it worked fine.
However, that situation can be averted by installing
NTFS-3G for Mac OS X - after doing that, my drive is detected every single time, without fail.
Generally speaking, though, it is advisable to use FAT32 if you're going to be working across operating systems. The alternate solution would be to install the proper HFS/HFS+ drivers so Windows can read Mac volumes (or if Linux, the proper ext2/3 or maybe ReiserFS support, although Reiser doesn't have Windows filesystem drivers, IIRC). Like I said, because Windows, Mac, and Linux all recognize FAT32 volumes without additional software, that is the easiest cross-platform option.