As mentioned in the comments, the cf card in my alix died right after the installation, and I decided to hook up a 2.5” hard disk instead.
Getting the disk was trivial, it is a standard notebook hard disk, which can be bought almost everywhere.
Getting a 44pin ata cable to attach the disk to the alix board was a problem, after some weeks I ended up getting the cable totally overpriced on ebay due to lack of alternatives.

The harddisk *has* to be slave, even if you do not have a cf card attached, you can't have the hdd being master.

I was scared of temperature and the missing space between the connector strip and harrdisk, so I decided to piggy back the harddisk.
To do so, I had to saw a hole into the case for the ata44 cable and drill some holes to bolt down the disk.

The disk is bolted down centric, the cable had to be split in segments for more flexibility.

Disk speed is useable, not a rocket, but given the overall performance of the system it is enough:

dd of=/tmp/1G if=/dev/zero ibs=1M count=1024
1024+0 records in
2097152+0 records out
1073741824 bytes (1.1 GB) copied, 62.9221 s, 17.1 MB/s

hdparm -tT /dev/sda

/dev/sda:
 Timing cached reads:   380 MB in  2.00 seconds = 189.54 MB/sec
 Timing buffered disk reads:  152 MB in  3.00 seconds =  50.60 MB/sec

DMA seems to be missing …

hdparm -d /dev/sda

/dev/sda:
 HDIO_GET_DMA failed: Inappropriate ioctl for device

The test were run with linux kernel 2.6.35.6-delaware from robertalks.

But it is obviously possible to cram the hard disk inside the alix 2d13 case, as shown by the pictures of Veselin:

The 44pin cable plugged next to the CF card.

The 2.5 on top of the CF card with the 44pin cable tucked underneath.