If you are economizing, here's a simple rule:
Do buy a CPU/motherboard one or two levels lower than commercial state of the art.
For best value, look in the middle of the current range of available processors. On the desktop, in late 2007, that means a CPU costing perhaps $75 to $200, not the latest and greatest quad core marvels selling for several times that!
Why? Because of the way manufacturers' price-performance curves are shaped. The top-of-line system is generally boob bait for corporate executives and other people with more money than sense. Chances are the system design is new and untried — if you're at the wrong point in the technology cycle, the chip may even be a pre-production sample, or an early production stepping with undiscovered bugs like the infamous FDIV problem in early Pentiums. You don't need such troubles. Better to go with a chip/motherboard combination that's been out for a while and is known good. It's not like you really need the extra speed, after all.
Besides, if you buy one of these gold-plated systems, you're only going to kick yourself three months later when the price plunges by 30%. Further down the product line there's been more real competition and the manufacturer's margins are already squeezed. There's less room for prices to fall, so you won't watch your new toy lose street value so fast. Its price will still drop, but it won't plummet sickeningly.
Again, bear in mind that the cheapest processor you can buy new today is plenty fast enough for Linux. So if dropping back a speed level or two brings you in under budget, you can do it with no regrets.
Consider one drive rather than two. This will reduce overall system performance somewhat, but the cost saving as a fraction of total system cost is often substantial.
Another easy economy measure is looking for repaired or reconditioned parts with a warranty. These are often as good as new, and much cheaper.
Your display is one of the areas where pinching pennies is not a good idea. You're going to be looking at that display for hours on end. You are going to be using the screen real estate constantly. Buy the best quality, largest screen you possibly can — it will be worth it.
Similarly, do not reduce the amount of RAM in your system too far. A minimum of 4GB of RAM is helpful in desktop systems today.