Individual Applications

For individual apps, the best way is filing a bug requests or feature request in the individual applications.

Some upstream development portals might be having explicit feature for asking user ideas but most of them use their bug tracker for that.

Example, you want a new feature in Synapse (the kick-ass launcher powered by zeitgeist) then you can file a bug request, ask for the feature and ask for the bug to be classified under [Wishlist].

Or before filing bugs for wishlist, you might want to talk to the devs of the particular application. You can look at their mailing list or IRC channel.