Flying is a game breaker. It however also can be controlled. Like many things where 3e removed a 'gotcha' limitation on spell powers, it resulted in unnecessary brokenness. I can't speak to 4e because I'm not familiar, but I would suggest the following.
1) Spells are one of the most common ways to gain flight. It should be explicit that if you are flying when the spell is dispelled, you are automatically falling. 3e removed this drawback, much to its loss in my opinion.
2) Flight, and in particular flight with 'Excellent' or better manueverability, is generally underpriced in my opinion. Either reduce the quality of magical flight from spells directly (or make the manuevarability scale with level of caster, with poor manueverability generally available early on), or else increase the level of the spells (or both).
3) Long duration always on items are generally underpriced in 3e. In particular, you are much more likely in my games to find an item that lets you cast a spell on yourself X times per day, than you are to find an item that grants you unlimited access to that spell. A 'ring of invisibility' that lets you be invisible all the time and has no drawbacks is IMO, something that shouldn't be showing up at all before very high level and should be priced under the item creation guidelines accordingly. In particular, the 3e item creation rules don't take into account balancing factors of the spell like the normal length that the spell lasts when determining what the spell should cost when made effectively 'permanent'. There is relatively greater advantage in making a spell that lasts rounds last 24 hours compared to making one that lasts hours last 24 hours. At lower levels, a 'ring of invisibility' or 'ring of flight' that let the wielder use a spell once or thrice per day is much less abusive and more likely to be balanced with the rest of the campaign.
4) Magical mounts are under the above obviously much stronger choices than they would be otherwise. Of course, magical mounts have obvious drawbacks that obviously under default 3e rules deprecate their usage relative to a 'ring of flying'. If you have a magical mount, you are vunerable to having your mount shot out from under you. You also have to pay the penalties to hit with ranged weapons for using winged flight, and you probably have insufficient manuerability to fly around in a typical dungeon. Still, if 'dispel magic' is reasonably common (and it should be) and 'always on' magic items relatively rare this might be worth it. At a metagame level I find this highly desirable, because wing mounts have alot of mythic resonance.
5) Both ranged weapons and spells have unrealistically large ranges that also have the undesirable effect of creating tactically simple situations. Since reducing ranges improves both my simulation and game, I've reduced both weapon and spell ranges to make melee a stronger option, which in turn reduces the number of monsters that simple go down hard at range flying or otherwise. As a nice side effect, spell ranges now tend to be inside weapon ranges, which makes spellcasters somewhat more vunerable.
Flying is not all great though. A flying creature cannot take cover. In balanced encounters involving ranged weapons, the ability to take appropriate cover is often the determining factor. Beyond 'having the high ground', a flying attacker is actually at a considerable disadvantage in a ranged weapon fight. One thing I find is that outside of an ambush, any encounter intended to challenge mid-high level PC's must have a ranged fallback option because really, flying is just a special case of the general 'maintain your distance and pummel option'. Giants need to throw rocks/spears. Humanoids need to have ranged weapons. Outsiders better have a ranged attack of some sort whether spells or missile weapons. If you build monsters like you would build a PC, with a primary attack/strategy (ranged or melee) and a fallback if the primary attack is unusable, it tends to go better. It also tends to go better if you mainly put monsters in terrain they are effective in. This is both gamist and simulationist as well, as a monster with reasonable intelligence is going to choose a place to lair which suits it, and a monster that can't stick to terrain that suits it probably will have died before the PCs came along.
However, I think that too much focus is being placed on how flying is a game breaker during combat. This is the least of its problems. Flying also does the following:
1) Gives you a +100 bonus to climb checks and grants you a natural climb speed.
2) Gives you a +100 bonus to balance checks and makes you trained in balance.
3) Gives you a +100 bonus on jump checks.
4) In the case of wingless flight, gives you a very large bonus on move silently checks.
5) Gives you the ability to avoid pressure plates and all traps based on gravity.
6) Allows you to move across difficult terrain without penalty.
The biggest problem with flight IMO is that it gives you the equivalent of epic level skill in several areas. The poor skill monkey or martial class working diligently on his athletics in order to do these awesome stunts, finds himself immediately outclassed to an incredible degree by a relatively lowly application of magic. His utility to the party which formerly had been quite high is suddenly reduced to a very low level. He isn't needed to climb the wall and throw the rope down anymore. He isn't need to find the pressure plate. He doesn't get to shine as the only one who can make it across the ice covered chain to pull the level. This is a problem skill monkey classes ('thief') have been having since 1e.
