I introduced elements from the BoED when my players were just about to make 6th level (so they could take exalted feats at 6th level). They just made 12th level last weekend, and I don't think the rules have unbalanced the game at all.
In some cases it has helped them (in certain specific cases, greatly so), and in others it hasn't made a difference. They haven't been in any encounters that the rules from the BoED have been detrimental to the party, except for the ranger with the Vow of Poverty feat. He has been "shunned" by the nobility and many of the well-to-do, and the help that they have to offer has turned to other "well-groomed" individuals. So his role in the city has changed dramatically.
Some of my observances:
Certain properties of the BoED are automatically beneficial in the normal Good vs. Evil campaign. If your characters are good, then their enemies will most likely be evil. Hence, many of the feats will obviously be helpful to them, knowing that they will be facing a lot of evil baddies. But, since I will tailor-make bad guys to go against them, its just fair to let them prepare themselves as they see fit.
For example, the Sanctify feats do extra damage to evil creatures. Good guys will fight evil, so this would stand out as fairly helpful.
The Vow of Poverty feat would be extremely unbalancing in a low-magic, low-treasure awarding campaign, and it probably shouldn't be used in that setting. However, in the oposite extreme, a high-magic, high-treasure awarding, magic-shops-on-the-corner type of campaign, the feat could leave the character slightly behind the rest of the party. And... if you award more treasure than standard, the feat will be weaker. Anything in between, and the feat should be just about standard when compared to the equivalent character equipment-benefits.
The benefits beyond the benefits of the VoP is that the character doesn't don armor when hastily awakened. He doesn't have to worry about his gloves of dexterity being stolen. Or destroyed. Or dispelled. And that applies to all of the benefits that replace magical equipment that a character otherwise would have.
As for how I brought it into my game:
I told my players a few weeks in advance that I was working them up to an encounter that would allow them to take exalted feats, and that I would allow the majority of the BoED into the campaign. I wanted them to be able to look at their characters and make any adjustments to their character path, if desired, to be able to become an exalted character.
I ran
Fallen Angel, from the WotC website, to introduce them to some trumpet archons at the end of the adventure. The trumpet archons gave them "the blessings of Celestia," and opened the door for them to use the BoED.
(As a campaign note, I am running the Adventure Path from Dungeon magazine, this encounter occured about the same time that Alek Tercival was meeting the "trumpet archons" near the Demonskar. When the group's paladin met up with Alek next, they were both swapping stories of blessings from trumpet archons. By the time the party finally made it to the point of drinking the elixir, they bought it hook, line, and sinker.

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From a role-playing perspective:
The party ranger made the biggest change in character concept. His character had been, up to that point, very self-centered. Very "an eye for two eyes," if you catch my meaning. He began the transition to a good-alignment the next week, giving him some time to role-play it in.
After he took his first vow, I told him he would have to work his way up to the VoP feat by slowly getting rid of his equipment, trading away his magic items for mundane, his magic weapons for masterwork (at first), and donating all of his treasure to charities. (He chose a soup kitchen for the poor and the various temples, primarily St. Cuthbert.) When he gained 9th level, he was met by an avatar of his goddess, and she swore him to the VoP, taking the rest of his equipment and leaving him with almost nothing. It also gave me the opportunity to tell him, in game, that he would be bound to the vow, and that he would lose all the power granted to him if he were to forsake them.
The role-playing aspects brought into the game from the BoED have been outstanding, and very rewarding to the players who use it. The feats, of course, have made the party well-prepared to face the onslaught of evil that they have encountered, and that too is very rewarding to the players.
As DM, I feel rewarded by having the players care enough about my campaign, that they are interacting with their environment (role-playing) and taking the time to prepare their characters for the challenges that await. We're all having a good time at it.