The Dio2496 works with Alsa. It is not very common, but I have spoken to people using the Dio2496 along with an ART DI/O for the DAC on Linux. It is discontinued, but easily found on eBay. As another poster mentioned, the M-Audio Audiophile PCI is the same chipset, and has coax digital in/out.
I don't know about M-Audio Transit. The M-Audio Sonica does not have a proper firmware on the device and requires proprietary software to upload the firmware before it will work, which prevents it from working on Linux. The Transit may or may not require this.
I am not familiar with the DeQ 2496.
As far as Optical vs Coax vs AES digital (AES uses the XLR connector, but is a different impedance than regular mic cables if I remember correctly), go for coax. AES is better for long distances than coax as it has better electrical noise rejection. I generally recommend coax over optical because you can get by cheaper than optical. RG9 coax cable commonly used for cable TV works well for short-medium distances, and is the proper impedance (75ohm) for the SPDIF standard.
Also, Parts Express is an excellent source for digital cables, optical or coax, plus you can also stock up on good stuff like Neutrik headphone jacks and audio grade capacitors/resistors