Intel DG45FC mini-ITX motherboard w/ Titan TTC-NK54TZ CPU Cooler*Right click and view/save these images to see them in their original larger size!*The Titan was chosen because it fits in our little case and is rated to cool sub-100W quad core CPU's. Coming in at 39mm in height with its 10mm fan, it is quite space saving... even when compared to the low profile stock Intel heatsink normally shipped with their 65W CPU's which is 1.875" [48mm] in height as shown below.

System-Hive Logix Mini-ITX Case (of course)
-Intel DG45FC mini-ITX Motherboard
-Intel E4600 2.4GHz Dual Core LGA-775 65W CPU
-2Gb G.Skill DDR2-800 1.8v RAM
-WD 160Gb 2.5" "Black" HDD
-2x2.5" Hot Swap Bay
-Card Reader I/O Multi-Function Panel
-Titan TTC-NK54TZ CPU Cooler
-2x60mm Vantec Stealth Fans

Right off the bat, the Titan's heat-pipes created install issues as they stick out too far on one end limiting the orientation this cooler can be mounted on a mini-ITX motherboard. They either bang into the RAM on the front, the caps on the back, the north bridge cooler on the left or the case wall on the right.
This is a pretty big oversight and I can only speculate as to why this is. Were the heat pipes bent at the wrong location? Did they have to be soldered to the CPU plate close to one end of the pipes for them to function properly? Was the heat pipe a standard length part that didn't quite fit in with their design? If you look at the pic, it appears that the curve in the pipes could have been formed so the ends come out equally thus having less of a bend sticking out on the other side to cause fit issues.

So the only thing that can be done to make it fit is to shave off a row of fins on the north bridge cooler. This is as easy as it gets as far as mods go. Heck, you could snap them off using just your fingers. Using an Enzotech low profile copper heatsink would have been a more elegant solution... if only Intel had decided to use the standard two push pin clip mounting system instead of their own cowboy spring clip design.

The good news with the Titan... along with the fact that it kept the CPU in the low 30's C which makes it worth the trouble of modding it onto the board IMHO...is that you can put any 80mm fan on it. I tried several fans up to 80x25mm in size and all fit in the case. Note that the closer the fan gets to the cover and the higher the fan RPM's... the louder it draws air in throw the cover vents. This can be remedied by adjusting the fan speeds but the Intel mobo made this a challenge.
The Intel DG45FC is a great little board with it's socket 775 and DDR2-800 support, DVI, digital audio and e-SATA ports that can be used for anything from an HTPC, home/business computer or even industrial applications. The one major shortcoming however (outside of Intel's typical refusal to offer overclocking options) is with its fan control.
In the BIOS, there are some cryptic fan speed options called "Zone Response" and "Zone Dampening" with settings such as slow, normal and aggressive which appear to have no discernible effect. The result is always the same... the CPU fan runs at full speed and the case fans run at 4V. Pretty much every fan that I know of is rated at a minimum of 5-6V to run them at their lowest speed so I have no idea what Intel was thinking. Your rear case fans will simply hover between just barely running to not running at all until the board senses the temps reach some unknown value in the stratosphere. Also note that the fans may also constantly cycle back and forth from the lowest to fastest RPM's if you don't have the latest BIOS installed.
The hardware will obviously stay cooler with the bloody case fans actually running to provide a steady flow of fresh cool air through the case. They don't have to be running 100% to accomplish this. Just a nice steady quiet stream of air around 14 CFM. Second, the cooler works very well so the CPU fan does not need to constantly run at full speed. This would obviously be desirable for people who bought this board for HTPC use!
So what are our options? Surprisingly, none of the mainstream fan controlling software (like Speedfan) appear to support this board. There are several miniature "set and forget" in-line fan speed controllers available (see link below) so you can disable Intel's version of cool'n'quiet (this is done outside the BIOS using a dev kit I believe) and ramp the fan speeds down to the desired RPM's. This will unfortunately disable temp and fan RPM sensing but what can you do. You can also get fans that are designed to run at low RPM's at their highest voltage. I personally prefer using fans that can run at higher than needed RPM's so you have some headroom to ramp down to the best balance of RPM's, airflow and noise.
http://www.frozencpu.com/cat/l2/g47/c17/list/p1/Fan_Accessories-Fan_Controllers.html?o=price_ascHere is the installed system. Note that I'm experimenting with the multi-function panel we sell that can read 62 card types and has an excellent array of ports... the most notable being front audio ports with internal connectors which none of the ones at NewEgg appear to do.
http://hivelogix.com/bay-devices/multi-function-panel
Demonstrated once again... a great deal can be installed into this box... even with mid-level skills in cable management.

Let me know if you have any questions and feel free to post any info that pertains to hardware compatibility with our mini-ITX case in this thread.