I've been over this ground a bit myself. I favor baronies or small fiefdoms for characters -not JUST a castle, but also not an entire country. I don't know what level of detail you may be looking for but here's my two coppers on the books I own:
Stronghold Builders Guide was one of my favorite D&D 3.0 books. It gives a lot of options for a PC stronghold builder but it doesn't focus on the realm-management aspects or accounting. I would use this book if I wanted to build a house or manor, especially if it had a lot of magical acoutrements. (Or if it was a flying or underwater stronghold). It also has templates and descriptions of typical rooms and layouts, which is handy for those who don't know everything there is to know about medieval fantasy architectural conventions.
Strongholds & Dynasties (which is third party, so may not meet your criteria) puts less emphasis on magic use in stronghold construction and magical enhancements to the stronghold. The Dynasty system is focused more on a small kingdom (multiple fiefdoms / provinces).
Birthright was a more abstract approach to ruling a "domain" which some may prefer. Also interesting because it divides between religious, magical, economic ("guild"), and law holdings. However the domain system could be almost a game in itself, and of course the system resembles nothing in 3e. I highly recommend the Book of Regency even if you don't use the birthright system - it was available at one time as a free download, and may still be. Try googling birthright book of regency.
Magical Medieval Society (also third party) provides a good system for running a very specific type of smallholding (an agricultural, western-european style fief), but the amount of detail may be too much for some. Also despite the term "magical medieval" the focus is more on the latter (it is, to my mind, more like history with a thin veneer or magic, unlike, say, Ptolus, which is a more "integrated" scheme). However anyone trying to run anything other than a western european-style manor will be left out in the cold (okay, so this is the income for barley and this is the income from rye - what if I want to run a fishing village?)
Way of the Daimyo is nice but very setting-specific. It assumes Rokugani social system and economy, which is great if you're running a Rokugan game, otherwise, not. The differences are least apparent for military lords and most apparent for arcane casters. (It would be an excellent resource for a monk PC stronghold builder, though).
Castle Guide almost completely ignores the role of magic and is of very little use in terms of ruling a domain.
So I recommend the Stronghold Builder's guidebook without reservations. The others will depend upon how macro you want your approach to be & how big of a domain you plan on running.