Dali

You can find the server here

1.1. User interface, on-line help, choice of parameters and databases
Very easy to use, just download the structure if you have new versions of browser (bigger than Explorer 5.x and Netscape 4.5), otherwise email submission; no other possible operation
1.2.Interactive versus E-mail results or notification
both options for uploading the file and the results are delivered only in e-mail form
1.3. Documentation, access to literature references
on the main page there is a original paper describing the method and small old review(1994) about a structural comparison both in html format.
1.4. Confidentality
I haven't found any information
1.5. Elapsed time between submission and results
Usually very fast (4-8 minutes), but eventually can be slow and take a few hours (probably because of high server load)
1.6. How long are the results kept on the server ?
As long as you don't erase them, since the results are sent through email

2.1. What information is reported for the hits?
It contains PDB ID of similar structure, z score, RMSD, number of equivalent residues and others. List is sorted by z-score. Lines and rows in the list of the hits are disordered in Outlook email program, less disordered in web-based email programs - difficult to orient.
2.2. Measure(s) for goodness-of-fit and statistical significance?
Z score- strength of structural similarity in standart deviation above expected
2.3. Structure-based sequence alignment?
yes, structural alignment in text format (list of equivalent fragments between structure), not very friendly (very tough to find needy information)
2.4. PDB files with superimposed structures?
not directly from results, only possibility is from Dali domain dictionary, but only with known structures, not with new structure
2.5. Interface with visualization software?
, but there is a very well shelter hyperlink to Rasmol software at help page, almost impossible to find
2.6. Hyperlinks to the other web-based resources (e.g., PDB)
only to FSSP from results and to FSSP and Dali domain dictionary and MaxSprout (reconstruction of full coordinates from C-alpha trace) from main page.

3.1. Are there parameters the user can set to optimise the results?
No
3.2. Is there a choice of database? How much of the structural universe do they cover?
no, it searches in the subset of PDB (contains structures with sequence identity less than 25 percent), but it is not easy to gain this information, only if you submit structure by email you can meet this information
3.3. How often are the databases updated?
the same as PDB's frequency of update (once a week)