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There are a couple of things you can try in order to speed up your code.
First of all, when you need to loop through a collection, create a view where you have all the values you want to check against in the different columns. Then create a NotesViewEntryCollection instead of a NotesDocumentCollection, and loop through it using GetFirstEntry() and GetNextEntry().
Another way to perform lookups is to use lists. If the number of entries to check against is reasonable small (I have had lists with up to 20K entries though, IIRC) you can use IsElement() to perform a check. The list tag has to be unique, and should be what you are looking up, while the list item value can be the UniversalID of the document, or even a NotesDocument object (but that will take up much more memory, so use the UNID instead).
You could also narrow down the collection using the FTSearch method of the NotesDocumentCollection class.
Finally I would use Teamstudio Profiler and check what part of the code is still slow, and see if you can tweak it even more.
Feedback response number WEBB9EYKU6 created by ~Dan Kikiterobu on 01/02/2014