Loremaster isn't quite a feat every other level - you can't take the same secret more than once, so you can only take Applicable Knowledge once. Some of the other secrets are pretty nice too, though.
Anyway, Paragnostic Apostle is definitely worth a look. It's a five-level class with entry requirements easily met by any character who wants to play that role (K: Religion, Arcana and any one other Knowledge at 5 ranks each, cast 3rd level spells, membership in the organization) giving full spell progression, d4 HP, 4 skill points per level, and more importantly every level the class grants a special ability from a predefined list. The special abilities all require a certain number of ranks in a given knowledge skill, and are minor boosts to spellcasting that are generally freely usable. They're somewhat weaker than feats, at least in my opinion, but of course you get one every level. For example, there's one that grants your summoned creatures Fast Healing 2. Or one that grants a +1 to hit with any ray attack against a creature with a natural armor bonus.
The class also grants Lore/Bardic Knowledge, with levels in the class counting double. Or, according to a plausible but clearly broken reading of the text, all levels in any lore-granting class counting double.
Flavor-wise, it requires membership in the Paragnostic Assembly, which is an organization closely associated with the Church of Boccob. It does require some minimal amount of religious affiliation, but Boccob's church is described as being interested in knowledge more than in devotion. Higher ranks of the organization require a somewhat onerous tithe, but there's no real need to advance formally if you don't want to.
The class works for clerics as well as wizards - it grants continued turn undead progression, although it doesn't grant the ability if you didn't have it to begin with - but the d4 hit die pushes it a bit more towards wizards.
Complete Champion also has the Knowledge Devotion feat, which sounds like something else the player might be interested in - it allows you to gain insight bonuses to attack and damage rolls based on how well you roll on a Knowledge check to identify a creature. Freely usable, and if you can get your Knowledge results up past 35 it's a +5 bonus. The bonuses aren't restricted to melee attacks or weapon attacks, so they'll boost spell damage as well.
As another possibility - is this for an existing character? If not, has the player looked at the Archivist? It's a divine spellcaster that uses a spellbook, but more importantly the Dark Knowledge class ability sounds like the kind of special knowledge the player is looking for. It's in Heroes of Horror, but it's also available as a free preview on the Wizards web site:
http://www.wizards.com/default.asp?x=dnd/ex/20051007a&page=3
There are feats in Heroes of Horror to expand the types of creature the ability works on.
