Generating neat orbitals/surfaces from molden/wfn-files
Often different quantum chemical programs require different analysing tools. Unfortunately there is no universal standard (program), that can do it all. If there were, someone would come along and just invent something new.



I personally prefer ChemCraft for producing publication ready images. It is a commercially distributed program. It mainly supports any Gaussian and GAMESS file formats (and Firefly by extension). It can visualize quite a few more formats now. What I especially like about the program is that it can read the files generated by the NBO programs. It makes visualisation of all kinds of localised and canonical orbitals much simpler.
There are some more features of the program I really got attached to, like symmetrizing molecules or building molecules from scratch. It has the big advantage of writing the symmetry adapted data group for GAMESS for custom basis sets, which I have not been able to find anywhere else. But this is certainly not the target of this post.
 Unfortunately it is not able to read molden or wfn[1] files.  

The program comes with a large number of visualisation schemes, which can easily be modified to produce a personalised style. Below is a small demonstration.


Most of the times I would use one of the above, depending on whom I have to impress. Often it is far more beneficial to have monochrome images, like the ones below.


A quite recent addition came with styles that allow you to generate simple 2D like structure. It is still possible to overlay these structures with orbital plots. (Unfortunately the transparency is hard-coded and cannot be set explicitly.)


The caveat is obviously, that it cannot read molden or wfn[1] files, not even Turbomole output.

A feature that I am still missing is the batch production of orbital pictures. You still always have to save them by hand, which can be incredibly tedious for large molecules (and large active spaces). (But I have written a feature request for that.)
Support for the program is quite good and the available help files are even helpful. Most of the features can be understood intuitively, however, as always, it takes time to get used to working with it.
Another caveat is, that the windows version outperforms its little linux brother by a lot. If you already run windows somewhere, that is probably fine for you. If you run linux almost everywhere, then you have to deal with some missing features (or recently it can be ported via wine, making it slow though).



I do use molden (Xwindow) quite a lot for intermediate visualisation, since it is one of the fastest interfaces available. It is very robust and has low graphics; you can easily use it whit a rather slow internet connection. It is free for private and non-commercial usage. Since my first days as a computational chemist involved the use of 56k-modem for checkup routines, this was one of the only go to programs. It will always be the first program I install on a work-dedicated computer. One simply does not forget his or her oldest friend.
A very big plus is the very well structured and written postscript files produced by molden. Some of the purists might even like it. Here are a few converted samples, but you can download the source here (via tinyupload.com).


Such files can become extremely handy, when preparing posters (especially when using LaTeX). I have on occasion seen molecular plots generated by molden in publications; I am even guilty of that. However, nowadays I believe there are more elegant methods.



Visualising Turbomole output has been, is and will probably always be a painful experience. For some of the deeper features you should probably be an expert in gnuplot, too. For the basics of structure and orbitals, the current recommendation is to use TmoleX, the GUI to turbomole. If it is done by the same people who designed define, then it's will be quite painfully to use. When I was a heavy user of turbomole, this did not exist, so I should probably shut up.
Judging from the current (version 7.0) manual the workflow I used is still somewhat recommended. It is to let the native modules create the binary *.plt files, which are gOpenMol input. Unfortunately, what was once a very aspiring program is nowadays not developed any more. You can still obtain an unsupported copy. The source code is available, but the current license state of the program is somewhat unclear. Since VMD (see Brians post) and TmoleX do now support gOpenMol files, the necessity of learning a deprecated program is probably not useful any more. One of the prime features of this program however was that it has a tcl interface and hence was fully scriptable - apparently something that VMD now also has.
It is well capable of producing nice orbital pictures, you might have seen them on this page already. (I tweaked the Gaussian output a bit, since I do not have Turbomole available.)


Although it supports quite a few file formats, molden input and wfn[1] is unsupported. 



[1] Let's come to the last part: wfn files. However you produce them, they are probably not up to date. The main (and probably only) purpose for those files is the analysis with AIMPAC -  a program that is no longer developed. They have one very big disadvantage: they cannot deal with functions higher than of f type. If you are using a triple zeta basis set, you probably have those functions. Another disadvantage is, that they don not include information about possible effective core potentials.
For the purpose of analysing the electron density with the quantum theory of atoms in molecules (QTAIM) the much superior version wfn extended (*.wfnx or *.wfx) should be used. I am currently only aware of Gaussian to create such files correctly. The main program which uses these files is AIMAll. It is also a commercially available program. You can learn more about these files on the specification page there.
The only valuable point of creating molecular orbitals with this program is, if you want to overlay it with the bond paths instead of just sticks. Just like in this example:


Apart from this usage, the process is very tiring and needs many steps to be completely performed. Working the program non-local is very, very slow. And to be perfectly honest, what is the purpose of the above other than impressing a few organic chemists?
Another negative aspect of the program is the very high demand of memory and storage, especially for large molecules.

In conclusion: If you are not doing QTAIM analysis you should probably refrain from *.wfx files for visualisation purposes. For every QC program there usually comes a workable interface/visualisation program. With any program there is the activation barrier of learning how to do things to overcome. In any case, I suggest having a few ready to work with, you never know where you go and you might have to learn a new program any time.
I think the biggest loss of any visualisation tool is the neglect of writing good tutorials or even a basic documentation.