The number one enemy of your custom PC is heat. Overheating is very easy when you put together components yourself. Overheating will shorten the life of processor and motherboard. Worst of all, a faulty processor or motherboard can be working intermittently and hard to troubleshoot.
I know because I lost a CPU due to mild overclocking, which means heat. Luckily it lasted long enough and that's time to upgrade. So I swapped the motherboard and CPU altogether. I had the next system broke down in about 3 years, perfect timing for upgrade again. So I didn't bother whether the CPU broke down or the motherboard.
The next pentium 4, 3GHz, became faulty after a year, when I forgot to turn off some video software turning a firewire camcorder into a webcam. It cost me dearly as the system worked perfectly for some random time and then reset. I wanted to save time and so I asked the Firedogs at Circuit City to diagnose my PC. It was a waste of time. Even worse, because I couldn't imagine that they couldn't test the processor properly, I never thought that my processor was faulty. If I didn't ask them for help, I would always guess that the CPU was faulty. I ended up returning the motherboard twice for nothing. I finally get a new CPU from Intel. It was rather painless - all components were under warranty. Service was quick and I only paid forward postage.
Firstly, get the right components to avoid overheating. The new BTX cases are BIG. But you can get away with fewer fans at lower speeds, meaning quiet operations. The most popular by far are still ATX cases, but the current ones fit for 3 GHz CPUs are bigger than the ATX cases for the first Pentium 4 processors. However, I don't suggest spending a lot on brand new cases. Old cases can still be used with additional fans probably installed. Fans are cheap and quiet, but it's always quieter with less fans.
Enermax has some high efficiency power supplies, which should mean less heat dissipated to the surroundings. I can't tell the difference from the field but this could be important if your PC is put in a confined space. There are some supplies with modular connectors. You take out the connectors that you don't need. But they are expensive. They are not really needed if your case is big enough to hide some unused connectors near the top.
ATX cases hold ATX motherboards and the smaller micro ATX boards. The bigger ATX boards are naturally better in dissipating heat. Also ATX boards usually have a total of 3 fan connectors while mATX boards has two. Though you can easily connect a fan directly to a +12V output of the power supply via adapters.
I don't play much games so I opted for integrated graphics on the motherboard. You can also have integrated ethernet and firewire. I normally have no extension cards to generate heat and obstruct air flow.
Use only two drives if possible, a hard drive and a DVD/CD/drive/burner. The only reason you need two hard drives is for RAID. And now with matrix RAID for newer chipsets, two drives are all you need for faster access times in some partitions AND mirrors in other partitions. If you stack two typical 4 inch (width) hard drive top to bottom, the heat is phenomenal. Try to separate them as far as possible.
And yes, dump the floppy. The cable just obstruct you and the air flow. Newer motherboards can make use of USB flash drives the way they make use of floppy drives.
Serial ATA drives are wonderful. SATA2 at 3Gb/s are sustainable 1.5 times faster than ATA100 IDE drives. With SATA available for DVD drives, forget about the 40 pin 80 wire connectors. They are torture to install in comparison. More importantly they block airflow.
To test your system you need to be able to measure the temperatures. All retail motherboards come with sensor for the CPU temperature and motherboard temperature. They all comes with utilities so you can monitor the temperatures in Windows. To be sure, get SpeedFan from download.com to measure the hard drive temperatures.
It's preferred to put your PC at the floor near windows, it's cooler this way. Since a PC is a big toaster, I suggest that everybody should install a humidifier nearby to save your skin if you work long hours by the monitor. It's also cools the air.
Leave the case open and leave the PC running idle for 20 min or more. All temperatures should stabilize around 40 deg C or less. It's usual for motherboards to sound alarm when temperature reaches 45 deg C. Drives temperature should not be above 50 deg C. If heat is not accumulated, temperature should not rise or drift slowly upwards. And the drive temperature will be close to the motherboard temperature. Unless of course you stack two or more hard drives together.
Then run anti-virus programs to exercise the CPU and hard drive. Except for the CPU temperature, the other readings should not increase by a deg or two. The CPU temperature should be stabilize at less than 50 deg C, though 60 is the alarm threshold. The motherboard has to be cool enough for the smart CPU fan to work. It's no use blowing hot air on the CPU when the motherboard temperature keeps rising.
Finally close the PC case to see how much the temperatures rise. If the motherboard temperature rises a few degrees, that means you can benefit from installing more fans.
If your PC is not cool enough, consider putting your PC against a wall, so you can leave that side of your PC case open. You can drop a few degrees that way.
If you need to install fans, follow the general airflow design of cases. Cool air is usually draw from the lower front of the case and extracted at the top back, where the power supply is. Your case should have places to install a fan at the front to blow air into the middle. Another place is right under the power supply, to help pushing hot air out of the system.
One more thing, the CPU heat sink comes with a thermal paste to make good contact with the CPU. If for some reasons the paste is gone, like installing a new CPU, you need to clean up the paste and get some thermal compound. They look like grease and can reduce the CPU temperature by 10 deg C, compared to no or hardly any thermal paste.