Mr. Rainman.
I am Mr. Locke, and I will tell you the difference between ISL and 802.1q trunking protocols... Simply put, ISL is cisco propietary, which means if a switch has some 802.1q trunks, and some ISL trunks, it will negotiate to the ISL. If ISL is proprietary, then why did they make 802.1q?
because 802.1q works with other vendors, i.e. Enterasys, 3com, etc... so if you are going to be migrating a crappy network to a cisco backbone, you will end up using 802.1q to span your broadcast domains into your existing switches, all the while still segmenting your network into broadcast domains ( number one reason for using cisco switches , in my book )..,,
so they both work, but if your using cisco to cisco , then use ISL, if not , use 802.1q.