From having played a Druid who only specialized in making his pet awesome and doing nothing else, some general things I've collected;
- Warbeast: Probably the most important one aside from Magebred. So long as your Druid can actually make this check (or lives in a world where NPCs can in place of him before he gets his companion). The downside is that, being a 3.0 template, it only mentions "animal, beast or vermin", beast being a removed type in 3.5 - so no to the Magical Beast type question.
- Magebred: Along with Warbeast is a great template for any Animal you want (or even want to be emulating via the Feral Rearing trick as a pseudo-Animal PC, but most DMs probably won't let that fly). Again, like Warbeast you want this template. The exception is, is that you as the character can't really just do it yourself - you'd have to buy one and make it your Animal Companion, or somehow work out with your DM that you're a breeder and have one. Like Warbeast, it works on Animals only (not Vermin as well in this case).
- Totem Druid ACF: From Dragon Magazine 335, this variant has two unique toys. First, although it may be against the spirit of the article - or really actually might be - you get your Totem Animal Companion at 1st level. This includes the tiger, dire eagle, bear and all the like - all at 1st level. Additionally, you count as your Druid level +2 for advancing your bonuses for your Animal Companion, or at what level you can make your Animal Companion selection Dire instead. It also provides you with Natural Spell as a bonus feat (at 2nd level no less!) and lets you get a continuous Speak with Animals (Totem Animal) spell and lets you talk normally while in your animal form at 8th level. The downside is you can only Wild Shape into variants of that animal (Tiger, Celestial Tiger, Dire Tiger, etc) and so on. The good news is that your Totem Shape (replacement for Wild Shape), "... uses the same rules as Wild Shape." so you could argue it qualifies for anything stating Wild Shape to some degree... just not very strongly. Overall, I love this variant, but it's extremely specific and narrows down some shenanigans.
- Feral Animal Companion: Costs a feat and is a small buff, but does some neat things in the shape of giving +2 Strength and Constitution to your Animal Companion, as well as allowing them to infect attacked victims with the Red Ache disease. Most interestingly, it gives a massive penalty to Handle Animal checks made by others toward your companion - it's a nifty trick, not too useful, but still a buff to your companion. The downside is, is that you're going to be a Neutral Evil Druid as it specifies you must be Evil to take it.
- Natural Bond: Boosts your effective Druid level by +3 for determining bonuses to your Animal Companion; this does not allow you to exceed your effective Druid level above your actual character level. If you're dipping something that doesn't give effective Druid levels for your Animal Companion, this is a way to compensate.
- Wild Cohort: While not actually an Animal Companion, it gives you a weaker version, who, in turn, you can be a Magebred Warbeast. Natural Bond should actually make the Wild Cohort's level equal to your Druid level instead of -3, and if you're a Totem Druid on top of it, your Wild Cohort should actually count as being valid for the +2 effective Druid level bonus as well. It's still weaker than your Animal Companion, but a lot better if you take Natural Bond and are a Totem Druid.
- Animal Defiance: You can turn creatures with the Animal type as a Good Cleric turns Undead, but can't destroy or command them. This also gives you 3 + your Charisma modifier uses per day of this ability as well as using your highest divine caster level to determine turning results. It's 3.0, but its still neat and needed for...
- Animal Control: Very 3.0 heavy (requires Animal Friendship spell), but it gives you more "turn" attempts, except that unlike Animal Defiance, these are counted separately and allow you to rebuke and command animals as an Evil Cleric commands or rebukes Undead.
- Tamer of Beasts: A 3.0 prestige class, but it does some really unusual things... Like give your Animal Companions gained through the Animal Friendship spell an Intelligence score of greater than 2 and making them Magical Beasts. I'm sure you can find a way to use this. It has a lot of neat features but nothing game breaking - I like it overall, but it doesn't progress your casting much and runs into issues of how to qualify for the class as well as actually use its features in 3.5. Overall, it does your Magical Beast request well, I think.
- Beastmaster: Like the feats that boost your effective Druid level and the Totem Druid variant that actually increases it, this prestige class actually gives you +3 more to your effective Druid level, netting you a total +8 if you use them all together, which can easily result in some silliness - just nothing too crazy or epic.
- Awaken: Specifically this spell says, "You have no special empathy or connection with a creature you awaken, although it serves you in specific tasks or endeavors if you communicate your desires to it." it states it actually will help you, and you could make a pretty convincing argument that you helped make them awesome. Remember that they don't keep any of the bonuses you provide though; they aren't benefiting from your Animal Companion features... except if you're a Tamer of Beasts. Now they're incredibly intelligent, sentient, and are benefiting from those class features as well. Good times. Again, you could easily make an argument to your intelligent Magical Beast ally that being "tamed" by your abilities only makes them better, and provided you weren't a complete dick or abusive, I don't see why they would disagree (aside from your DM being mad).
- Off/On Topic Note: Being Neutral Evil doesn't mean you have to be a terrible person to your animals. You might be selfish and cold to people (and or other creatures), or you can only care about number one, and by number one, you include the pieces of yourself; your animals. There's a lot of ways to handle that (unless your DM arbitrarily decides what Neutral Evil means in their game explicitly) but I strongly suggest that you always take good care of your bestial allies, especially if you plan on making them intelligent some day.
I'm certain there are more (Supermount and Hi Welcome for sure), but these are all what came to mind based on your request.
