Iron Heroes: This has character power and complexity roughly on-par with D&D, but it will take a bit of time for the group to get used to and develop a good grasp of the rules differences between D&D and Iron Heroes (stunts, scenes, combat tokens, etc.). Iron Heroes has no magic or hardly any magic (don't use the Arcanist class in there, it's broken and hastily devised; well, unless you want to revise it yourself, or spend a while searching the Web for revised Arcanists).
Use Iron Heroes if you want magic to be unavailable or nearly so; magic items can be used with it but are not necessarily required (unlike D&D where they are required). I think I remember the book titled Mastering Iron Heroes (IIRC) has some villain classes and other useful material for running the game, but I don't remember if it has any errata/replacements/facsimiles of the Arcanist.
Grim Tales: This is more flexible than D&D but generally low-magic (or no-magic if you want). It's a tweaking of the D20 Modern rules into a more flexible form, using talent trees and feat trees to customize characters. Probably your best choice if you want low magic, but that probably depends on how you define low-magic (since it could mean low-powered magic, infrequent magic use, rare magic use, or very limited magic, such as long and costly rituals or whatnot; I think GT is more of a low-to-medium level of magic power, and with less frequent magic use than in D&D, due to magic-induced fatigue or backlash damage or somesuch; I can't remember now what its magic limitations were exactly).
Warhammer Fantasy Roleplay: This is extremely grim and gritty fantasy fare. As shilsen and others have said before, this is the game where you start out thinking you're playing D&D, only to realize later that you're playing Call of Cthulu.
Fatalities are not that uncommon in WHFRP, and PCs are generally supposed to avoid combat most of the time for the sake of their own survival, but it's a cool setting and a cool game. Simpler than D&D. Magic in WHFRP is rare, especially since the character generation method is highly random (your starting occupation/background is randomly rolled, and it may be tough or impossible to advance into a spellcasting class if you're not lucky).
Also, magic use can potentially drive a character insane if they're not careful, and its generally best to resolve matters through mundane efforts simply to avoid that chance; but when the situation calls for it, a spellcaster can try and unleash magical devastation or some handy spell or another if he needs to. Magic can be devastating sometimes, but IIRC, the more magical energy you tap into at once, the more likely it'll draw the attention of Chaos demons and such, or the more likely it'll drive you insane. Characters get Fate Points to help them out, but they're a rare commodity.
I think that about covers it for the main ones. True20/Black Company is less crunchy and D&Dish, but still rules-medium I think, and I have doubts about how fun they'd be in the long-term (AFAIK, characters will tend to wind up pretty similar and dull after a bit, but that's just my opinion). Castles & Crusades is rules-light and based more on older D&D stuff, but I have even more doubts about how interesting characters will be after the first adventure or two. Again, IMHO.
Midnight is great and all, but I don't actually know anyone who's used the magic-using class or classes from that game, so I'm not sure how balanced/broken it is in that regard, all I know is that it's a very low-magic setting (only a few PCs/NPCs will have magic use, generally restricted to elves and evil priests if I recall correctly, and I think it's supposed to be tougher to work magic in Midnight, or maybe it's just less potent; but again, I don't know for sure, because I only know of one or two people who've replaced the Midnight spellcasting classes with a different system's magic).
D20 Modern itself could work, depending on what you're after. It has only 1 core book (though there are a few supplements for different settings; D20 Past for Westerns and Dick Tracy type stuff I think, D20 Post-Apocalyptic for modern or postmodern games in a devastated wasteland setting with mutants and such, D20 Future and its supplements for near-future and far-future games), and there are just a few supplements for the modern setting itself (Weapons Locker, Menace Manual, and maybe 1 other I'm forgetting). There's also the Urban Arcana hardcover setting book, but that's basically for playing D&D in a modern setting, using D20 Modern rules as a base (and generally considered not-so-good).
The D20 Modern core rulebook itself, however, has only a partial section on Urban Arcana, as well as a small section on Shadow Chasers and another on Agents of PSI, which are the three example campaign models. The Shadow Chasers section includes the Shadow Slayer advanced class (which is just a warrior with minor supernatural attacks/defenses for battling supernatural foes, as well as the ability to detect supernatural creatures nearby) and the Occultist advanced class (which is a scholarly sort who receives a few, free, magic scrolls as they gain levels, but that's about it; they have no spellcasting themselves, just the ability to use scrolls with a decent chance of success, and they gain minor Spell Resistance, and eventually, a very minor supernatural creature as a bound minion).
SC is for very low magic campaigns; no spells available to the PCs, just a few scrolls for the Occultist and maybe a few other magic items thrown in by the GM over time. The Urban Arcana section of the core book has a Mage advanced class and an Acolyte advanced class; these gain arcane/divine spells (respectively) of up to 5th level eventually, but no higher, and their class spell lists are slightly shorter than D&D's wizard and cleric. Mages gain a few minor metamagic abilities and minor magic item creation abilities, while Acolytes receive some turning/rebuking ability over time (initially just vs. undead, later against a few other creature types as well).
