Ok so I added 4GB more RAM to my Mac Pro, and I can definite see a difference in FCP (I can actually play the whole 1080p sequence at full quality without stuttering or beachball), and I was actually able to run FCP, Photoshop, After Effects, and Red Cine-X at the same time.. Something I am not used to!
But starting up applications still seems super sluggish compared to EVERY new mac in the apple store. I'm sure my HDD is part of the reason, but even a base 2011 21.5" imac with 2.5ghz processer and 4GB of RAM is significantly faster than my Mac Pro and they're both running HDDs.
What other variables are there? My Mac Pro is still running 10.5.8, could that make a difference? I always thought older models ran slower AFTER updating the software, but could mine running old OS be a reason?
Easy, replace the HDD. I will give you an example, I recently (unfortunately) purchase TWO hard drives, Western Digitals from year 2007. I paired them in RAID0 to get myself a speedy scratch disk. Guess what? The read and write times are around 80-90 MB/s in RAID0 !!!
Just to give you a comparison, I have 2TB WD Caviar Green in my Mac Pro also, this ONE drive gives me easily around 110-120 MB/s, and that is just single drive.
So if you are running original hard drive from 2006, you can imagine how slow it is. Technology has improved since then and also the older the drive is, the slower it gets.
If I were you, I'd buy 128-256GB SSD drive like Intel 520 or Crucial M4. These are reported as very high quality drives (you even get 5 years warranty on Intel) which are very speedy, so speedy that they might not even take advantage of your SATA bus. You can then repurpose your old mechanical drive for your iPhoto, iTunes library and other data files you don't need fast access to. SSD should have OS X installed and your applications.
You will see a HUGE difference and your Mac will be as fast as the new Macs in day-to-day usage. Believe me it will help a ton.
Even if SSD is too expensive for you, you can still buy Western Digital Caviar Black (1TB size seems good) and you will immediately notice the difference.
Remember, even if it seems like a big investment, you are able to take out SSD from your Mac Pro and put it in your next computer. Even if you decide to go with mechanical hard drive, you can probably do that too or repurpose it in external enclosure as a USB3/TB/Firewire drive.
I'm glad 4GB helped, if you ever get another 4GB you will see even more performance increase, especially if you have all those applications open at once (I put 16GB RAM in my Mac Pro and I can have like 20 applications open and it doesn't slow down).
EDIT: 10.5.8 is Leopard. It is widely believed that 10.6.8 Snow Leopard is fine tuned version of Leopard which runs faster on most of the systems. It will also give you Mac App Store and some other functionalities but I have heard from many people that Snow Leopard is faster than Leopard, has less bugs etc.
If you get SSD, do a clean install of OS X. You might have some clutter accumulated in Leopard from years of usage, the best way to get fastest system on SSD is to to a clean install on it.
The advantage of Mac Pro is that you have a lot of options.