I don't especially like mod classes, but on the other hand, I like customizing the classes for my world once and for all; and I also like having lots of classes, without caring too much for overlaps.
I use all classes from the Player's, beefed-up versions of the Aristocrat, Adept and Expert from the DM's, Psions, Psychic Warriors, all OA classes save Shugenja, all MiniHandbook classes save Favored Soul, and all AU classes. Plus a couple of homebrew.
What I also like is classes with subclasses. Like in AU, the Witch, Champion and Totem Warrior classes. And, to a lesser extent, the Samurai.
That's for reducing the need of multiclassing and prestige classing.
Another example of this is my magic system house-rule. It basically suppresses the need for a mystic theurge or an eldritch knight. I'm quite proud of it.
But for multiclassing, here's how I do it. You know, the values like BAB, saves, and MM? I don't use integers for them... A first-level wizard has a +0.5 BAB. In play, the +0.5 don't matter. It's just like +0. But if you then take a level of cleric, you get +0.75, and so you get to a total of +1.25. Which, during play, is the same as +1.
All BAB, saves, and MM (see my magic house rule thread) are formulaic. I've even modified the "median" save that is featured in some d20 game, but not in core D&D, to another progression (1 +2/5) for that.
For good and median saves, you get a +2 or a +1 at first level. This +2 or +1 is considered a "class bonus" and thus they don't stack with themselves when multiclassed, but they do stack with everything else.