I don't know of a way to "work around" the "one-click" thing. While I have used them, I'm not real fond of using them; it's so much "cleaner" to my way of thinking just to install most of those programs with the shell.
The other problem, in my opinion, is that the "one-clicks" also provides them with access to the list/creation of mysql databases (which of course you can limit with permissions, but it is not "seamless"). Personally, given the way certain of the "oneclicks" implement re-write rules, and other issues involving PHP4/5, etc, I have never felt comfortable turning a "sub-user" loose with that. I'd rather they contact me; I can spare the 5 minutes it normally takes to properly install any of those for them much more easily than I can spend the time it could take to "sort" it if they "bugger it up". YMMV!
As for the "filemanagers" out there, I have used several, and I think it really depends upon the sophistication of your user, and what you want to allow them to do as to which is best. For most of my needs, I seem to find myself using ffileman a lot; though the Gossamer-threads fileman is a "classic".
What I like the most about this approach, is that I can rely completely on the filemanager (which can be different for different levels of users!), and Dreamhost's use of suexec makes the use fo a filemanager (running as the user - yeah!) to "sandbox" the users' resources nicely. in conjunction with an ftp only DH user account, I think it is a reasonable compromise between giving the user "freedom" but protecting myself from anything they might do in the shell or the control panel. For me, it just works out better.
I have not really looked at many of the "newer" offerings; I'm sure hotscripts.com has scores!