I guess you haven't checked any port listings lately?
The majority of ports below 1024 (oh hell, almost every port below it, and quite a few above it) are reserved for use for specific programs. However, thats not to say you have to use those ports.
I can think of one good reason not to use ports below 1024.
Whilst the specific ports aren't secure, ports above 1024 are generally not actually used for specific purposes.