1) Do not invite citizen comment unless you have created realistic expectations about
a) how long it will take before someone can get to it,
b) how clear and articulated the comment/complaint needs to be in order to be interpretable and actionable,
c) what sorts of comments/complaints ought to be directed to that particular site/locus,
d) how likely it is that any individual comment complaint will be explicitly acted upon.
2) Do not invite citizen comment/complaint until such time, and unless, you are adequentely resourced for processing and dealing with them. Taking 18 months to reply because you have allotted 3 people assigned part-time to plow through e-mailed comments after they have attended to the rest of their job is NOT "open government", no matter how snazzy-looking the website is.
3) Do not invite citizen comments/complaints without examples to help shape their thinking and comments, and hopefully examples that have translated into actionable items, and actual actions. So, an illustrative example of "here's something a person told us, and here is how we were able to make this particular improvement because of it".
4) Do not invite citizen comments/complaints unless you are prepared to be honest and forthright in your replies, even when they are generic replies to a cluster of comments/complaints. No one likes a vague form letter that feels like a brushoff.
The bottom line is that you need to create the sort of environment where citizens will feel like they were heard, and where their expectations are not so unrealistically high that they feel unfairly treated. Part of that IS the response itself, and part is the manner in which their input is solicited. You can't act on things you don't understand, and without sufficient coaching, people won't always give you something you can work with. You need to help them out a bit.