Unlike some others I prefer not to list a mini/maxi series in with my top books of the year. Not because some of these didn't deserve listing. I just didn't want to give up the spot of a good series (Supreme Power) to list a mini (Adam Strange).
Here are mine in no particular order:
Adam Strange - a great sci-fi comic, something missing in today's market.
Ocean - see above.
Avengers: Earth's Mightiest Heroes - at least the Avengers I loved are still out there.
Secret War - not sure when (or if) this one will end but interesting so far.
Avengers/Thunderbolts - not quite a Thunderbolts fan but with Barry's art I could be.
Empire - this may be more a 2003 title but the last issue was released in January 04 (IIRC) and I loved this book.
Identity Crisis - as a whole I liked the series. Not too keen on some aspects and am unsure it lived up to the hype.
Formerly Known as the Justice League - another that just squeaked into 2004. Great fun, best Giffen since Vext.
League of Extraordinary Gentlemen 2 - I wish this could be an ongoing series of minis. And that I could forget the movie adaption.
30 Days of Night: Return to Barrow - I'm a sucker for a good vampire comic and Niles is the best in the business today for these.