In what format do you store your chess data? This question has plagued me for years, so I finally decided to blurb it all out. There are at least popular 3 file formats I can think of - Chessbase (CB) binary format (cbh, cbv, etc), Chess Assistant (CA) binary format, and standard text pgn format (with the spec here). Most other chess databases, such as SCID, Jose, etc also have their own binary formats, but I am not as familiar with those. There have also been a few efforts to represent chess databases in some open XML format, but of all schemas proposed, none has really gained enough popularity. At least most chess games available on the net are still available only in either PGN, Chessbase, or CA formats.
So what tools are available for dealing with each format? Virtually every chess tool can read pgn. Chessbase does not handle Chess Assistant at all, Chess Assistant allows you to read Chessbase format, which is pretty impressive, given that no other non-chessbase tool does that. So what are the advantages pgn format versus say, chessbase?
1) it is free to in the sense that you don't need a proprietary software to view its contents (SCID would do the job), has an open spec, so 'anybody' can implement a parser. There are few parsers available in source code (I managed to find c++, C# and perl parsers, there are probably others). That being said, I suggest you do not write your own parser, because it is not a trivial task, but rather take an existing one (of course as long as license is not an issue).
2) since PGN is text-based - one can just load them in notepad, as long as the file size is not prohibitively large.
Pgn is also very readable - the moves are just in algebraic notation. If you store your personal games in PGN, you can version control them as well, and look at the differences between revisions. It is also trivial to merge multiple PGN files into one via a one line in DOS.
So if PGN has so many advantages, why use anything else for storing chess databases? Why create all these compatibility issues between multiple chess database vendors? Same reason as why XML is not used as a backend storage for storing data in SQL databases - performance.
Chessbase format provides more than performance improvements though:
1) In addition to performance, filesize is also smaller - chessbase splits up databases into multiple files, and that allows for some normalization of headers, etc.
2) Multimedia support - one can embed audio and video into games.
3) it can be a real database - in addition to raw moves, chessbase stores other metadata, such as opening and endgame keys, allows to tag positions with so called "medals" and so on.
I have been using Chessbase light for storing my games since around 1998, and just don't want to lose all the tagging that I've added to my games for many years. So currently I maintain keep old databases in Chessbase format, and whenever I create new smaller databases (say, for selected games by Kramnik in the Sveshnikov), because Chessbase light can still edit them, performance is not an issue, and I don't have to re-export all games into PGN for using Palview.
An unexamined life is not worth living.