I'd say they can be worth it, and a lot of fun to play. A lot of it does depend on the class you want and how you approach the game.
Though for the most part, taking an ECL race does put a serious dent in a spellcaster's power. Still, I think it can be worth it for the other classes that rely more on combat and skills for their effectiveness.
As an example, right now I'm running a monk character in a party that is very heavy on the fighter-types (we have a paladin, a proto-duelist, and a wannabe mystic theurge) in a 32 point-buy campaign. Everyone is 5th level. I'm running a 2nd level, anthropomorphic tiger (from Savage Species) monk.
From a roleplaying standpoint, it's fun to play a character who's both an exotic curiosity to some of the more "normal" PC's, as well as one who is a sort of naive, fresh-out-of-the-monastery wanderer from WAY out of town. He certainly is memorable. From a mechanical stat point, the tremendous stat bonuses (+4 Str, +6 Dex, +2 Con, +4 Wis) balance out with the loss of 1 HD worth of hit points and the loss of one BAB point. In addition, since the character is effectively a multiclass Monstrous Humanoid/Monk, he gets the boost to his Reflex and Will saves, so they're really nasty. Racial skill bonuses help make up for the hit that he takes to skill points.
The end result is a character with respectable hit points (not as tough as the paladin, but then again who is), a fantastic AC (about 5 points higher than anyone else in the party), excellent mobility (unlike the armored fighters), and a not-too-shabby damage curve.
In the final analysis - ECL's can be worth it. What you want to do is make sure the benefits you get balance out with the hit you take in class features.