I think enforcing gender differences in a mechanical way is a recipe for disaster and hurt feelings, and I also think that @BESW’s answer probably indicates the best way to do it if you insist.
I’m just going to note here that there are a (very small) handful of cases where sex matters in 3.5. In most cases, these favor women, as it turns out. Forgotten Realms really likes its women (almost all of these are from FR).
This is the big one: by default (i.e. in Greyhawk; also holds in Forgotten Realms), Drow society is very sharply divided along gender lines, and the women dominate the men almost utterly. Drow women are far more likely to have authority, far more likely to have great wealth, and far more likely to have education and magical power than men.
All of this stems from the Drow goddess, Lolth, who favors women basically exclusively (Drow men are forbidden from being Clerics of Lolth) and also encourages extreme amounts of infighting in the race, which causes the women to use that favoritism to their extreme advantage.
This is represented mechanically by the Favored Class of the Drow, which is Cleric for females and Wizard for males. As far as I know, this is literally the only racial statblock in3.5 that references any kind of gender differences.
In reality, Drow make pretty poor choices for either class (or much of anything else, if we’re being honest), thanks to that LA +2. The +2 Intelligence helps Drow Wizards more than the +2 Charisma helps Drow Clerics, though. It pales in comparison to the social benefits of being a woman in Drow society, however. How significant this is in your game varies massively, however, as should be obvious.
Beloved of Valarian
Basically going with the “unicorns only appear to female virgins” thing, this prestige class from Book of Exalted Deeds is kind of like a weird hybrid Druid/Paladin in ten levels. Valarian, by the way, is a unicorn deity, and his beloved have “foresworn the love of mortals to dedicate themselves entirely to the unicorn deity Valarian, thus fostering a close bond with unicorns.” Your mileage may vary on exactly how squicky that is.
Hathran and Durthan
Forgotten Realms prestige classes from Player’s Guide to Faerûn and Unapproachable East, respectively. The Hathran are a sisterhood of spellcasters from Rasheman; the Durthan are Rasheman witches somehow related to the Hathran in ways I do not understand.
The Hathran are quite powerful, with full spellcasting, Leadership and bonuses to it, and Rashemi spirit magic. Rashemi spirit magic is basically insane, it allows a prepared spellcaster to spontaneously convert a prepared spell into any other spell they know, provided they are within Rasheman. At higher levels, they even get the ability to use it a few times per day outside Rasheman. Hathrans are also required for Rashemi Circle Magic, which is powerful, and high-level ones can lead a Great Circle, which is even more so.
The Durthan requires both arcane and divine spellcasting, but only advances one, so that’s pretty weak unless you trick your way past it (Magical Training plus Alternate Source Spell is a common trick). Still, she gets Place Magic, which is roughly identical to Rashemi Spirit Magic, though I don’t see any explicit restriction to having to be within Rasheman, which is absurd if that’s the case. The rest of the class features are much weaker than the Hathran’s, though.
As the name might indicate, within the Forgotten Realms setting, these spellcasters are almost only women. The prestige class does not actually require that the character be female, though. The only reason I bring it up is because Incantatrix is easily in the top-5 most-powerful classes in the game.
Weird 3.0 prestige class from Shining South, the Scourge Maiden is basically a champion of Loviatar, the Forgotten Realms’ goddess of pain. 3/6 spellcasting means it’s pretty awful. Gets the equivalent of Stunning Fist but for scourges, which upgrades to Nauseating and then Dazing, which is pretty solid (immunity to Daze is extremely rare, so it’s a great effect to inflict). Still, it’s only up to 6/day, so hardly amazing.
Another prestige class from Book of Exalted Deeds requires that you be female. You can turn into a Swan (à la Wild Shape), which isn’t exactly amazing, but hey, free flight. Also gets full BAB, good Fort, 9/10 spellcasting, a bunch of Spell-like Abilities (charm person, charm monster, speak with animals, and speak with plants), Wild Empathy plus bonuses to it, and type changes to Fey at 10th level, which comes with DR 10/cold iron. Not great, not awful, but it is female-only.
The only male-specific prestige class I can find, from Oriental Adventures. Entry requires being born male but losing your manhood, which is harsh by any definition. Some would probably argue that it’s worse than the Blood Magus in a world where death can be reversed...
Anyway, the class is awful: it doesn’t advance spellcasting, just gives bonus spells like the Dragon Disciple, but without the melee buffs that the Dragon Disciple gets. He does get to designate three spells as being permanently Empowered with no cost, and a two to become Maximized instead. Not even close to being worth the lost spellcasting, since someone who had just stayed single-classed would have had the spell slots to use those Metamagic Feats normally.