Ok, that's much more informative! You have three basic issues and I'd like to address their merits individually.
1) Low magic campaign balance. This I completely understand, you are playing a home-brew (or highly modified) version of a 3rd edition game. In a campaign world like Forgotten Realms or Eberron, wizards and magic items are in balance with the setting. But, like I often do myself, you have chose to either modify or make your own setting. When you do this you have to understand that 3rd edition D&D isn't set up for low-magic. It's a high magic setting and all the classes, powers, monsters, items and such are all balanced under that assumption. This isn't a fault, this is by design. Thankfully pen and paper RPGs are usually flexible enough to support the changes you are making. Unfortunately, its easy to underestimate the amount of reworking this requires. For my low-magic desert campaign (think Dark Sun with nearly no magic and no psionics) I ended up having to re-write large sections of the player's handbook, not just wizards... but powers of classes, feats, etc. In that setting I used, for example, I wanted magic to exist but to be all but unknown (a dozen casters in the entire world or so). So I changed spells from "per day" to "per week". With the fact that magic was completely unknown, the fear and confusion it brought out in people, this actually made wizards and other casters extremely balanced in the campaign. You'll need to find your own modifications or changes to make them work for your campaign.
2) Balance in relation to commoners and other "normals" in the campaign. This issue isn't a difficult one to handle by the RAW. Wizards should be treated as a highly trained and extremely rare thing. The education required for it is beyond our modern PhD. So yes, a wizard's spells can be beyond normal in the economy and in relation to the other abilities of "normals" in the game, but they are supposed to be. Most commoners have rarely seen magic, much less have an available wizard. They've heard stories... and maybe, at best, in a city they saw a wizard once. Can a single wizard break a village's economy... sure, but that's not a problem in my opinion. Wizards are and should be rare.
3) Fills other class roles. Yes, a wizard can use Knock to open a door, use Invisibility to sneak past guards, it can use Charm to talk a local official into helping, it can summon something to tank, etc. Yes a wizard can do all these things that rogues, bards, fighters, etc can do; but it can do them only a few times due the limitations of spell memorization. A thief can sneak anytime he wants, a fighter can tank an opponent any time he wants, etc; a wizard can do these things once or twice at best. I suspect part of the problem you are having is the same problem I had as a DM (though mine manifested in other ways): timing. D&D assumes a fairly fast, combat-based campaign, and all the classes are based around this (including wizards). In that hard-hitting action environment of encounter after encounter, a wizard shines... but only temporarily. It's a bright flame that nova's out and dims for the rest of the time. The other classes are a steady light in the action, always there, always reliable. Personally, I run a campaign based around intrigue and plots; in game time, days and days (sometimes weeks) will pass between combat encounters. In that kind of campaign, the daily spell restrictions on wizards and other casters are meaningless and it can throw the balance out. The issue here though is you and me, not D&D. If you are having the same issue, you, like me, have chosen the wrong tool for the job, D&D isn't designed to deal with that kind of campaign. Of course, it can be modified to work with such a game, but it will take effort and thought. In my intrigue and politics campaign, Detect Evil spells and their ilk are banned, as is ESP, and other things that demolish intrigue. Sure, I can have everyone involved have proper magics and magical equipment to mitigate this (I've done this in other campaigns), but I, like you, have chosen a low-magic campaign so that isn't appropriate. So my advice, is go with Rule Zero of the DMG... it's your campaign, change it to fit your needs. Get rid of ESP, change spells to per week or whatever you need to fulfill your requirements. Heck, perhaps adding a HP cost to spells (blood magic) or some other penalty might be best.
One last piece of advice: I don't recommend is that you do is make these kind of dramatic changes to an existing campaign. Start a new campaign with these rules up front and the players will know what they're getting into from the beginning. You might be able to pull this off with an existing campaign, but only if the players most affected are positively behind you on it. Otherwise you'll embitter them. When they picked wizard they had a mental image and expectations of what that would be based on the rules. Changing the rules is essentially you destroying those expectations and it's unfair on the player. There are things you can do to change the balance of power in an existing campaign if you feel it's a problem. Make sure the PC's opponents have as much access to magic as the PCs do, use the same tricks they are using against them... divination spells against the PCs can be particularly brutal in allowing the enemy to prepare. Introduce NPCs and property to the campaign... this gives you something you can use to squeeze the PCs with, especially the casters. Sure, the wizard can handle anything you throw at him, but what about his apprentice, love interest, servants, friends, etc? Give the player's a property... and have the NPCs use magic to breech it. You'll find your wizard begin to spend more and more of his resources (ie spell slots) to try to take care of those potential problems and less to take care of combat related or campaign related problems. Give it some thought and I'm sure you can come up with some solutions to these problems. The best way though is starting from scratch with a modified system that meets your needs.
-Arravis
