Creatures Can't Add Levels Because of Necromancy

Gazoo the necromancer can't just cast the spell animate dead [necro] (PH 198-9) and make any ol' corpse into a ghoul and add 2 levels of fighter to it. That can't happen. There shouldn't be any way to create creatures and, during their creation, add new class levels to them because of necromancy.

When the spells animate dead and create undead [necro] (PH 215) et. al. are used, the corresponding creature or template in the Monster Manual is used. For example, despite a necromancer being able to create 12 Hit Dice of undead, he can't create a ghoul and add to that ghoul 10 levels of sorcerer.

The game doesn't allow such shenanigans. Were such a creature permitted (in addition to a host of other problems it'd introduce), when the ghoul Sor10 is destroyed and the remains subsequently targeted by the spell raise dead [conj] (PH 268), the creature brought back from the dead would be as he was before he died plus 10 levels of sorcerer--and, of course, down 1 level because of the effects of the spell raise dead. Maybe, anyway. I don't know. It's impossible to say. The rules just don't accommodate things that the rules don't accommodate, y'know?

However, Creatures Can Keep Their Levels Despite Necromancy

The following undead can be created and retain the abilities they had in life. Some creatures have additional requirements for their creation beyond what's listed.

• The template bone creature (BoVD 184-5) is acquired via either the 6th-level Sor/Wiz spell create undead [necro] (PH 215) or the 8th-level Sor/Wiz spell create greater undead [necro] (PH 215).
• The template bone naga (SK 73-4) is acquired via the spell create undead.
• The template bonesinger (Gh 158-9) is acquired via the spell create undead.
• The template corpse creature (BoVD 185) is acquired via either the spell create undead or the spell create greater undead.
• The template crypt spawn (Mag 184-5) is acquired via either the spell create greater undead or the 7th-level Clr spell undeath after death [necro] (Mag 129-30).
• The template curst (LE 155-6) is acquired via either the spell create undead or the spell create greater undead.
• The template dread warrior (Una 62) is acquired via the 6th-level Sor/Wiz spell animate dread warrior [necro] (Una 43).
• The template juju zombie (Una 66-7) is acquired via the spell create undead.
• The template necropolitan (LM 114-5) is acquired via the Ritual of Crucimigration (LM 115).
• The template revenant (CSQ 127) is acquired via the minor artifact claw of the revenancer (CSQ 129).
• The template shadowslain (SSL 158) is acquired via the minor artifact shadow shard (SSL 152-3).
• The template silveraith (CSQ 127-8) is acquired via the spell create greater undead.

Only the bone creature, bonesinger, corpse creature, and necropolitan templates are from non-Forgotten Realms sources. (At a guess, that's because Faerûn has a greater number of higher level creature so more options were developed to exploit that resource.) There are, undoubtedly, other templates available as this list ignores Dragon and Dungeon magazine and Web content. Note: The template lich (MM 166-8) (and, by extension, the template lichfiend (LM 156-8)) is more the product of becoming rather than creation, but creatures with the template lich also retain the abilities they had in life.

"Specifically, What about Bonesingers?"
A creature who acquires the bonesinger template retains the abilities it had in life. The bonesinger template went largely unchanged in Ghostwalk's official D&D 3.5 update. The bonesinger template can be acquired by any creature with 1 or more levels in the bard class. When an appropriate corpse presents itself

A cleric of 12th level or higher can create a bonesinger with the create undead spell. The cleric or another person assisting must have at least 5 ranks in Craft (sculpture) and 5 ranks in Perform in order to prepare the body before the spell. (Gh 158-9)

Needless to say, if a PC necromancer knows where the bards are buried--especially if he knows where there's buried a dragon or something equally impressive who was at least a Brd1--he better get graverobbing now. Other necromancers'll swoop on those corpses fast.

"What's So Special about Skeletal Warriors?"
In the Dragonlance Campaign Setting--an official, licensed Wizards of the Coast source--is the template skeletal warrior (229-230). A creature who acquires the skeletal warrior template retains the abilities it had in life. To be eligible to acquire the template skeletal warrior the creature must be a humanoid with 3 or more class levels (not just Hit Dice). When a skeletal warrior is

created through arcane or divine magic... its soul is trapped in a golden circlet, which can then be used to command the creature.... The spellcaster creating the circlet must be a cleric..., sorcerer, or wizard of at least 6th level who possesses the Craft Wondrous Item feat. The golden circlet costs 60,000 [gp] and 2,400 XP to create and has a caster level equal to that of its creator at the time of its creation. (230)

Uniquely, the skeletal warrior template can be bestowed upon a corpse without casting spells, employing artifacts, or performing rituals--anyone with the feat Craft Wondrous Item (PH 92-3), money, time, and XP can bestow the template upon a creature.

Templates Acquired via DM's Discretion
Although each can only able to be acquired via DM's discretion, a creature retains the abilities it had in life when it acquires the template death knight (MM2 207-9), death knight of Krynn (DCS 212-5), dry lich (Sa 155-7), ghost (MM 116-8), gravetouched ghoul (LM 103-5), gravewright (StS 31), greater mummy (DD 159-60), huecuva (FF 94-5), keening spirit (CSQ 126-7), mumia (Gh 167-8), mummified creature (LM 110-2), pennaggolan (OA 189-90), sepulchral thief (Ci 133-6), swordwraith (FF 173-4), tainted minion (HH 153-4), umbral creature (LM 128-30), vampire (MM 250-3), and, probably, others, too, as this list ignores Dragon and Dungeon magazine and Web content. It just seemed a shame to waste this information.

It is generally assumed that when you relinquish control over the undead (which you can do, per Nox’s answer), they aren’t compelled to obey the last orders they were given, and therefore they don’t. Actually, it’s generally assumed they start terrorizing the populace and attempting to sate their particular hungers.

Strangely, however, nothing outright says this. Skimming the relevant sections of Libris Mortis, it’s stated that spawn gravitate towards their creators and will automatically return to servitude if a cleric disrupts that bond, but spawn are different from rebuked undead. No mention is made of necromancers’ control here.

That does, however, indicate the traditional approach here: delegated control. Through the use of the appropriate undead minions, one can effectively lead an army by controlling creatures who in turn control more creatures.

But since you are the DM, you could easily rule that this isn’t entirely necessary and that the player can try to use clever temporary applications of rebuke undead to effectively control more undead at once. It sounds like you find this interesting, which is the usual reason I wouldn’t recommend it: personally, I’d find it a headache to keep track of as a DM. But if you wouldn’t, then you certainly can do this. It does make the necromancer more powerful, but in a complicated and involved way, that should lead to more a more interesting game (unlike usual routes to extra power, which lead to a more boring game because it eliminates challenges).