If you're unsure of your ability to gauge too hard or too easy, lean towards to easy and make heavy use of "waves" of enemies, such as re-inforcements. That way, you can adjust the difficulty mid-battle, when you have a better dea of how things are going. Have the sheets and info for any NPcs in a second wave ready to go in case it's needed.
Try to make enemies with more defenses and health than offense, so if you misjudge the encounter and it proves too hard, the PCs won't get completely slaughtered before they can realize it and retreat. If your players use a lot of battlefield control and "save-or-lose" type spells, this might not be a useful DMing tactic, as such spells will bypass hp, DR, and resistances (and frequently enough, SR), making the low offense monsters into utter jokes.
Finally, sometimes it helps if you clue in the players to how tough the fight will be. More experienced players will have ome insight into what is "the boss fight" and such (unless the DM takes measures to foil their attempts at this insight). This is a useful skill because in 3E, there are a LOT of abilities that are of the /day usage type. Unloading a lot of these furiously can make a tough fight much easier, and holding back on them can make an easy fight more difficult. So, you could give a really fearsome description of the things you're concerned may be too strong to encourage them to go all out on those monsters. Alternatively, any fight where they're losing badly, they'll probably start tossing out their highest level spells and such just to survive anyway, so it can be self-balancing. If after such a battle, you had more planned butare concerned they lack the resources to handle it now, let them rest or scale back the following encounters in difficulty.
Once you have more experience, take a look and compare some numbers. Look at a monster's attack bonus and compare to the ACs of the players, most importantly the ones he is likely to attack the most (ie, a hill giant will likely end up pounding it out with the Fighter; a drow archer would likely try to pluck off the mage or healer). Look at average damage dealt and compare to hp of players to estimate how many hits they could survive. (To find the average of any even-sided die (which will be nearly all of them), simple divide by 2 and add 0.5 -- average of a d6 is 3.5, d8 is 4.5, etc...).
If it has SR, can the casters overcome it 50% of the time? 25%? 75%? Will it's energy resistances/immunities potentially make the mage ueless in harming it? For some it won't matte,r but for evocation types, this can be important to consider.
If it has DR the melee characters don't have the proper weapon to bypass, is it a lot? How much damage will the melee PC's attack do after DR? If the PC's main way of dealing with DR is Power Attack, be careful the monster doesn't also have a high AC, or else the Fighter may have a lot of trouble harming it.
If you have a Rogue who relies a lot on Sneak Attack, any enemies immune to it will severely reduce her effectiveness in combat.
And so on... always keep in mind your group's specific strengths and weaknesses when figuring out how hard an encounter will be. And it's ok for the Fighter to encounter a high AC and DR foe, the Rogue to face undead, the wizard to find a golem, etc... from time to time. Not every fight has to ensure all the PCs are unhindered, as long as the others in the group can contribute and you're not stacking the deck against a specific PC too much overall. --If half of all the enemies encountered are sneak attack immune, you would be screwing over the rogue, for example.
