Anyone know what is the best hardware Raid for Debian? Two as well as four channels? I am quite worried about hardware compatibility as normal support list of motherboards or raid cards seldom mention Debian.

Generally, if it works with Redhat or Linux in general, it will work with Debian. Redhat makes some performance/compatibility tweaks to their kernel, but it's mostly the same at the core.

3ware and Adaptec controllers have strong Linux support, but many others will work.