1. Start w/ a good case.
2. Avoid gimmicky coolers that block case fans exhaust.
3. Use a Heat Sink and TIM that near the tops of the list.http://www.silentpcreview.com/Recommended_Heatsinkshttp://www.frostytech.com/top5heatsinks.cfm#INTELHEATSINKhttp://benchmarkreviews.com/index.php?option=com_content&task=view&id=432&Itemid=62&limit=1&limitstart=23http://benchmarkreviews.com/index.php?option=com_content&task=view&id=492&Itemid=62&limit=1&limitstart=4
pick a TIM from the top few here:http://www.hwreviewlabs.com/index.php?option=com_content&view=article&id=64%3Amega-44-thermal-paste-round-up&catid=32%3Around-ups&Itemid=47&limitstart=3http://www.xbitlabs.com/articles/coolers/display/thermal-interface-roundup_10.html#sect1http://benchmarkreviews.com/index.php?option=com_content&task=view&id=138&Itemid=1&limit=1&limitstart=3
4. Understand the realities and myths of lapping, air flow direction TIM application. For example:http://benchmarkreviews.com/index.php?option=com_content&task=view&id=492&Itemid=62&limit=1&limitstart=2
5. Be neat with cables ..... sleeving multiples cables in a common sleeve is a good way to reduce clutter.
6. Keep heat sinks, fans and components free of dust.
7. Dump Molex connectors....snip, snip....yes you can use adapters but their bulk results in a a bundle of flow blockage. I either unsnap the molex connectors off or snip them off when I am stuck with them and solder on new 3/4 pin connectors. Better yet, buy case fans with 3 pin connectors. Enthusiast MoBos typically have fan headers rated at 2 amps while most case fans draw about a third of an amp. Provided you have checked your ratings and left some headroom, you can gang common fans (i.e. twin rear case exhaust////twin case from intake) on a single header.
8. To control fans via MoBo, you'll need a MoBo that provides the feature....not all do.
9. If you have connector issues , lack of MoBo features, or whatever, you can always use one of these:http://www.newegg.com/Product/Product.aspx?Item=N82E16811992005