First, a word about some mechanics: I strongly suggest that you only create “LA +0” races, that is, races in line with the usual choices presented in the Player’s Handbook. If your interested, I’ll explain what I mean below, but feel free to skip it if that’s what you intended all along.
3.5 has a rule called “level adjustment” (LA) that in theory allows players to choose “extra powerful” races without actually being more powerful. Basically, the idea is that an XYZ Fighter 1 is as powerful as a Human Fighter 2, so XYZ has “LA +1,” that is, counts as one level higher than its class levels for the purposes of its “effective character level.”
The long and short of it is that LA doesn’t actually work. Typical LA +1 races are better than normal races in some ways, but the resulting character (having a lower class level) winds up significantly weaker in some other ways, resulting in a skewed character. This is bad, I think, for the game. Thus I suggest only having LA +0 races (that is, the default playable case; note that “LA: –” indicates that a monster is not playable).
On designing LA +0 races
The first thing to remember is that LA +0 races have only minor abilities; your choice of race isn’t usually that important to a character’s mechanical identity, particularly after the first few levels.
All LA +0 races have a “net zero” to ability scores, that is, if they have +2 to one ability score, they have −2 to another. Having +4 or −4 are very rare and should only be granted with caution (since you have to assume that players may try to build a character who uses the +4 stat heavily while ignoring the −4 stat), but having two +2’s and two −2’s is pretty common.
Bonuses to mental scores, especially Charisma, are somewhat rare. Considering that spellcasters are the most powerful classes in 3.5, this is probably a wise precedent to follow, though ultimately +2 to their primary spellcasting score won’t really change things too much.
Wizards also occasionally “overvalued” Strength: see the Half-orc, which combines +2 Str with −2 Int and Cha. The Half-orc is generally considered very weak, and Strength isn’t actually worth more than other ability scores, so I don’t recommend following this precedent.
Also, having no ability score modifiers (as with Humans) is generally a drawback; the +2 should usually help more than the −2 hurts, so not getting any +2 is a penalty. Worth keeping that in mind.
Bonus feats are usually the best things you get from LA +0. In fact, the Human, with its freely-chosen Bonus Feat, may not be the best choice for a given class, but it’s almost always the second or third best choice (and frequently it is the best choice). This is why Humans don’t get any ability score changes. If they did, they’d wind up being the best choice an enormous amount of the time.
Pre-chosen bonus feats are still a really good deal, though, but it depends heavily on what feat you get. The feats that give +2 to two different skills are basically worthless; races can and should get skill bonuses, but they should be racial bonuses.
Weapon proficiencies are usually pretty weak because a lot of classes just give out all of those (and if you’re in a class that doesn’t, you probably don’t want to spend a lot of time wielding a weapon anyway). Nonetheless, weapon proficiencies are what you get from a lot of races; the exotic-weapons-as-martial features are better than the free proficiencies with martial weapons, for whatever it’s worth.
On the other hand, things like Power Attack, Two-weapon Fighting, the various Improved combat maneuver feats, and so on, are usually a bit better than what races usually get, and are typically feats that players are going to choose at 1st level anyway. Using these kinds of feats would give a slight boost to the significance of one’s race choice, which may be desirable, but if you want to keep things in line with existing material they’re not really a good choice.
So you probably wind up with some stuff that are minor, but useful. Skill Focus, Weapon Focus, Combat Expertise, Combat Casting, and Point-blank Shot are frequently used as “gateway” feats, being required for other feats or prestige classes, but are not terribly good on their own; those may be appropriate.
Saving throw bonuses
It’s pretty common to see races give +1 bonuses to all saving throws, or +2 to certain types of saving throws. These are useful abilities, but be careful that they don’t run into the problem of players forgetting that they are there if you go with anything that’s conditional.
+1 attack bonuses with certain types of weapons, or against certain types of enemies, are fairly common. I like the former, but not the latter, for the same reason I cautioned against conditional bonuses: it’s too easy for players to forget the bonus is even there when they happen to be up against the type of enemy they get the bonus on. But with weapons, since most players use one type of weapon for most attacks, that’s more frequently useful.
Skill bonuses, usually of about +2, but up to +4 if it’s only to certain uses of a skill, are very common. These can be applied pretty liberally without upsetting balance, since they are rather minor. Again, I prefer bonuses that are not conditional.
Most races get their own language as well as Common as Automatic languages; you should probably maintain that because having a party where some people are unable to communicate is a headache. Bonus languages are very minor, but you should give all races at least 4 to account for high Intelligence characters.
Personally, I detest the multiclass penalty mechanic and therefore ignore Favored Class, but that’s another story. “Flexible” races like Humans get Any, other races get some single class. If you’re including extra classes from supplemental material, it may be a really good idea to include two or more Favored Classes, though (races released later in 3.5 sometimes did this), where you use whichever of the set has the higher class as your Favored Class. That allows a bit more flexibility.
But I really do recommend ignoring those rules entirely. Maybe grab some of Pathfinder’s Favored Class rules; they did more interesting things with it.