Oriental Adventures 3.0
The Samurai Base Class as presented in the Oriental Adventures is a modified version of a fighter, with higher skill points, the Ancestral Daisho class ability, and a smaller list and smaller number (the samurai gets one every three levels rather than every other level as a fighter does) of bonus feats from which to draw upon, as determined by which Clan the Samurai originates.
All Samurai start off with a masterwork set of daisho and the ability to enhance it upon reaching level 4. The enhancement ability however requires the samurai to spend exactly as much gold on the enhancement as he would have to purchase such an enhancement. And rather than relaxing while his weapon is in the shop, the samurai must spend every waking moment (the exact amount of time required to enhance a weapon the old fashioned way) preforming the ritual required by this "class feature."
Complete Warrior 3.5
The Samurai Base Class as presented in the Complete series is a heavy armored two-weapon fighter specializing wielding both swords of the daisho simultaneously. The Samurai's class abilities are mostly derived of feats geared towards him wielding the daisho effectively (Quick Draw, Two-Weapon Fighting tree), as well as Kiai Smite and Staredown.
Those abilities aside, the Samurai has the same HD and Skill Points as a Fighter, but none of the versatility. It is also stated to be left up to the DM's decision as to whether the player begins with a masterwork set at all.
Assessing the Differences
The Samurai in the Oriental Adventures is balanced and works fine, as is (other than the sub-fighter feat progression), in the 3.5 rules. Author James Wyatt produced errata for the majority of the Oriental Adventures book in Dragon Magazine #318, only changing the Samurai in making the daisho honorable weapons. Furthermore, the Oriental Adventures is set specifically for adventures set in a Japanese campaign or setting allowing for the ease of integration.
The Samurai in the Complete series is an attempt at a culturally neutral version that could be used in any campaign without making them specifically Oriental or Human in feel or design. With the lack of options and the railroading of Samurai into heavy armor, many players believe the Complete Warrior Samurai to be inferior and suboptimal to even the 3.5 Fighter, which is also viewed in a suboptimal light. Compared to the Ranger, the Samurai gains TWF too slow, Quickdraw too late, and not even the Kiai Smite ability is seen as redeeming.
Like all other classes, the Samurai was created to fill a niche role. Like the Ranger, the Samurai is to be able to dual-wield; like the Fighter, he is to be able to run the gamut from light to heavy armor; but unlike both, his weapon are pre-chosen and his Kiai Smite ability and Staredown alone make him unique.
Ultimately, the classes as presented are up to the individual players choosing and the DM's approval for their campaign. But a good player will maximize on what they feel makes the class more suited to their playing styles.
Playing a Samurai
Using either class, players should remember that the Samurai is both a Caste system and a Class. A Samurai-classed character could be a completely devoted warrior or knight errant without mystical powers (as noted by the 3.5 Complete Warrior Samurai). A samurai-classed character could even go so far as to be a 1920's homage to gangs.
Picking a Prestige Class
Because of the inherent differences in the classes, both have different choices for Prestige Classes.
Oriental Adventures Samurai:
Complete Warrior Samurai:
Prestige Classes for Both