A monster that I have mentioned before is the molesti, an insectoid critter from the Oathbound setting from Bastion Press and Epidemic Books. It has the ability to spawn once per day and make some major alterations to its offspring. Officially there are just two, better armor and more limbs, but I have used spelltouched feats as other modifications. I have a few creatures from 3.X books (and one 3.0 and one Pathfinder) that I think would be better using the idea of modified offspring. The actual modifications come from Distant Horizon's Eclipse supplement. That source uses character points with 6 being the equivilent of a feat. Some of the modifications cost less than 6 and some cost a lot more. So for each creature, I will mention how many points they can invest in their young. After the creatures I will mention some of the possible general abilities and combat enhancements from Eclipse.

Note that all monsters that modifiy their offspring must have an intelligence of at least 8 and a lack of genetic superiority. In other words, beholders and other "perfect" monsters will not be willing to do this even if they could.

Molesti from Mysteries of Arena (3.5) and the Oathbound Bestiary (PF) have 18 cp.

Ophidians, from the Fiend Folio, are snake-like creatures that breed not through eggs but by spreading a disease. Normally ophidians are fairly blah because the transformation is complete- this isn't a template. Because they are so blah, I would give them 24 cp.

Zenthal mindshredders are in the MM III. They are wierd looking, hive dwelling aberrations that produce larvae that can transform into warriors and the warriors into more zenthal. The modifications apply to the warriors and zenthal, not larvae. They have 18 cp.

Briarvex are humanoid plants from the MM IV. They are known to breed in large numbers and overwhelm everything else that resists the spreading of their seedlings. In addition to 6 cp, they can convert their Entangle at will power into an additional 12 cp. This allows bands to have defensive and offensive members.

Tusked terrors are from the MM V. They are very intelligent, very fast pigs. They have way too much intelligence for what they are currently so I think making them a bit more magical with an additional 6 cp might be a way of making them more interesting.

Poukai are large, carnivorous birds from the Penumbra Fantasy Bestiary. They have the same issues as the tusked terrors yet I think they would do better with 12 cp.

Gryphs are in the Pathfinder Bestiary 2 (and Tome of Horrors for 3.0 and 3.5 and come from the 1e FF). They are parasitic birds that lay eggs in other creatures. They look and seem magical, but I think they need a 6 cp boost to really bring that out.

As for the general abilities (a small section of what is in Eclipse):

Acrobatics allows the combination of several physical skills relating to motion (tumbling, jumping, etc.) into one roll. Briarvexes and gryphs would benefit greatly from this, the latter using it to implant more quickly and effectively. The plants could use it for small teams meant to strike and fade while more durable siblings take the brunt.

Adaptation is to any environmental stress. This isn't just heat and cold, but can include talking to hostile crowds, zero g (examples in Eclipse) and such. Mindshredders, tusked terrors and poukai could use this to expand their territories. Ophidians could adapt to cities, hiding in plain sight when this is combined with Inherent Spell, Traceless or something similar. Adaptation allows them to live without fearing the human(oid) population.

Celerity increases movement rates. This gets expensive but it can be highly useful to all monsters that modify their young. It would be pointless for tusked terrors, at least as the basic form. Some of the upgrades, which allow for walking on water for short distances and similar stunts or adding a new movement rate (the latter is too expensive for them, unless the DM calls otherwise).

Costly is an odd one. It increases the number of slots or power points needed for a spell or power to affect the character completely. Fail to pay and the result is weaker than normal. Poukai need to defend themselves against tribal shamans who hunt them, and so they could use Costly.

Damage Resistance gets very expensive as it applies to normal DR and energy resistance. It can be modified to make it cheaper. All monsters would find it obviously helpful, but the gryph is weaker than the rest and could really use a leg up in preying on more powerful characters.

Grant of Aid is weak healing for a limited amounts of time per day. It can be boosted to fast healing but it still has limitations. Tusked terrors, poukai and gryphs would find this very useful as none have hands and thus can never gain or use the Healing skill.

Inherent Spell allows for a limited amount of low level spells the monster has in addition to its normal allotment (and there are upgrades that allow for the spells to become supernatural powers, additional uses and higher power spells). Molesti should have this as the setting they are from has over abundant magic. Mindshredders and briarvexes have the brains to use magic more effectively than the others.

Immunity applies to anything, from the very cheap immunity to jellyfish poison to the very expensive immunity to gravity for melee strikes (i.e. knock an opponent off the planet, requires DM okay). Briarvexes and mindshredders could produce limited numbers of their species with specific immunities meant to deal with local problems.

Innate Enchantment gives the monster the power(s) of a magic item. This is the one that I would use for the monsters without hands. Of course which magic items allowed depends on the DM and the monsters' innate knowledge of their possibilities.

Mana is too complex to explain here. It is additional spell slots, power or even the ability to alter reality (plus much more). Useful to every creature, this is the ability that really brings out the magic in a monster.

Mindspeech allows for telepathy and versions thereof. Since all of the monsters are intelligent, they can all use this. Even the birds could use it as a distraction or lure for weaker prey.

Occult Sense adds blindsight and such, though some are more expensive than others. Ophidians can have a snake-like ability to see heat and the birds could hunt at night.

Presence makes others cower when the monster is near. A few mindshredders, briarvexes or tusked torrors with this could really make a difference on the battlefield. Upgrades make the monsters overwhelming to weak opponents, easily routing them.

Resist is increases to saving throws. This should be used by all of them, the survivors who can give their offspring a better chance at keeping alive in the face of whatever killed some or most of the previous generation.

Skill Focus is important for the upgrades, which allow for stunts relating to the skills (though they cost spells, power or mana).

Spell/Power Resistance. The comment for Resist applies here.

Stoic keeps a monster going after death (well, with an upgrade). Gryphs could use this to breed one last time and mindshredder warriors are meant to die on the battlefield.

Traceless is another complex ability like Immunity. It allows the monster to do something (and each something is 6 cp) and there is no ability to track them. Ophidians that want to live in cities need this to survive. Mindshredders would want this for scouts so that they do not leave trails back to the hive.

Travel allows for unimpeded movement because of environmental conditions (as well as several upgrades). Briarvexes, molesti and tusked terrors looking for new hunting grounds (colony starters) would find this invaluable.

As I mentioned, these were but a small fraction of what Eclipse has to offer for character and monster design. There are also combat enhancements and metamagical theorums (though I am not going to mention any of the latter) as well as several new magic systems and spells over 10th level.

Combat Enhancements

Augment Attack provides additional damage or attack bonuses in specific situations. It is the upgrades that matter the most- crippling, disabling, continuing damage and more. Mindshredders and tusked terrors are the monsters most likely to use these in any numbers.

Defender increases armor class. The comment for Resist applies here.

Fortune is evasion but there are three versions, one for each save.

Imbuement, with enough cp, gives the monsters' attacks magical weapon qualities. Scary to think of tusked terrors, briarvexes and mindshedders with this.

Rapid Strike increases the number of internerate attacks. This is useful only to high hit dice monsters- molesti, mindshredders and tusked terrors (as well as advanced others).

Trick allows for special kinds of attacks- paralysis, death, fear and similar. It could be used to give a monster poison and all of them could use that. Consider a paralyzed victim in a gryph flock...

Modifying monsters can be fun, allowing the monsters to make the modifications themselves can allow for some really freaky encounters that will make the players pay attention. And that is an important point I want to make here- most of these modifications should be visible or otherwise open to detection. That allows the PCs to have some chance at survival, especially when dealing with large groups with diverse powers.