To me, the most basic, thought useful features are the following:
1. adding personal user library fields or changing the label of standard library fields (options/library&folders/standard user fields respectively user library fields)
e.g. I have user library fields for the type of release (CD, LP, 12'', 7'', 3''), the release's catalogue number (FOKUZ 017, MADDOG 03, etc.) and many more things.
2. adding view schemes for every occasion, say, a scheme that shows you files where certain information is missing, a scheme that dosn't show you files that are mixed or live, etc, enabling you to find anything you may be looking for without digging.
This can be done easily by right-clicking on the 'audio view scheme' then adding a 'new view scheme'. The window that opens up is really user-friendly and easy to use.
Along the way, I have just found out how nice it is to have a separate view scheme for tagging. If you enable 'tagging mode' with 'F4' you can tag directly in the pane with very few clicks.
3. You can adjust the look of MC, for example where the pane should be, what entries you want to show up in the organisation tree, the font and font size, etc.
4. You can customise pretty much everything in MC so it suits your taste. I.e. you can set up the startup volume, the startup window, what information your top display (player display) shows, how long the fades between tracks will be, etc.
5. You might want to change the library backup location to point to a safe location that you backup regularly another disk.
6. Adding a default audio editor like Soundforge so you can cut/sample your tracks in another software with nothing more than one click. (To set this up: Right-click/send to/send to (external)/add edit programs)
7. Organising your file names the way you want them (sounds like cosmetics, I know, but it costs you only a few clicks and can be pretty handy if something goes wrong)
Select the files you want to do this to, right-click and select 'rename files from properties'. In the window that opens you can define everything you can imagine using functions.
I have disabled the 'use "assorted" for artist on multi-artist albums' option and use:
[Album Artist (auto)] \if([Label, 0]=[], [], [Label, 0]\/) [Album Artist (auto)] - [Album] Field(Catalogue Number, 0)\ for the directory, and
if([#, 0]=[], /([Type][Disc Number]/), ) [Artist] - [Name] for the file name. Confuses me every time I look at it, but works perfectly in adding things like the label or catalogue number to the path as long as there is a correlating entry in your standard or user library field. If the album has more than one disc, MC even adds '(CD1)' or '(LP2) to the beginning of the file name, which I really like.
In this thread you will find more infos about it:
http://yabb.jriver.com/interact/index.php?topic=45704.0
I'm sure you will be making use of most of those things already. If you wanna make true magic happen I am probably not (yet) the right person to ask, but I hope some of it was useful to you.