How about making som design changes to the site manager?
I've got a bunch of sites now and I don't want to mix them up.

A folder system like in FlashFXP would be great. At least one folder level deep would be much better than what we have today.

Still love the program though :)

-nicmar

The idea is as good now as it was when I first heard it (1 1/2 years ago?)!

Basically we will then need to move the storage of those details from the sqlyog.ini file to somewhere else.  
Most likely a sqlite database.  And that would actually give a lot of more options (sorting, filtering, statistics ...).

However this is 'mid priority' only.

Really?
Why not like this:

[Categories]
Cat1=Private
Cat2=Clients
Cat3=Work

[Connection 1]
Name=Sitename
Cat=Cat1
...

That would be enough to begin with, one level categories. Although a redesign of the site selector would have to be done.

You could even do like this:
[Categories]
Cat1=Private
Cat1-1=Private Localhost
Cat1-2=Private Live sites
Cat2=Clients


Or is it more complicated than I like to think? :)

Could be done like that of course.   

However with details stored in a SQL database, we could do a lot of things (sort, filter are obvious but consider autocomplete, usage statistics, 'connection quality statistics' etc ) with little cost (except for the Query Builder that will come anyway!).

However nothing is planned in detail.  But we do realize that the Connections Manager can be pretty crowded.  
Up to around 20 connections is OK in my opinion. The design is not good for more.  But that I think is also more than enough for 95-98 % of users!