He wasn't saying it was the best. He was saying it's the most used, therefor there is the most support/releases for it currently.
Personally I'm a big fan of the 1.0 source (it's very well organized, fairly complete, not tooo many bugs and most are minor and from what I've seen it's quite stable. )
5095 CoEmu is rather stable but not much of the stuff is finished (systems and packets are missing such as guilds/trade/view gears/vending/mining/gw/pk events etc)
Lotf is very unstable, horrible organized but has tons of released stuff (usually very poorly coded making the server even less stable and worth using)
new lotf... it's better than old lotf from what I've heard but it's still not that great... bad organization, some bugs, really fucked up calculations... just not that great for the features you get. You would probably spend more time trying to correct the stuff in new lotf (assuming you can track down all the problems) than you would fixing up an earlier source that is already more organized and somewhat more stable.
As for data storage, I really have nothing against mysql, depending on how it is done: Yes it could cause some issues but I've never really had any problems with it. It's easy to do I/O from a database and personally (I have very little exp with .ini/.dat storage so correct me if I'm wrong) but you can layout your data far easier by creating new columns and changing around data types. without having to back to your data loader and completely re-write it simply because you added a new column...
I don't think stable is a right word for comparing these sources, but I would say 5165 is the source that is used the most. (IMO)