Manual of the Planes provides the tools for creating cosmologies (which were reprinted in the 3.5 DMG, but not in their entirety), gives a very thorough description of the default D&D cosmology (The Great Wheel), as well as a number of alternative planes and a few alternative cosmologies. Additionally, it has (3.0) stats for quite a few planar creatures, and four prestige classes. There are no magic items or feats, and only a handful of spells. The accent is on fluff and crunch that supports fluff.
Planar Handbook, on the other hand, is more in lieu with the Complete X series. It has prestige classes, feats, spells, and magic items. It also has monsters, a few planar city descriptions, and a very large (and utterly wasted) portion of the book devoted to "planar touchstones," planar sites which PCs can visit to gain REAL ULTIMATE POWER. Needless to say, planar touchstones suck as a concept, and suck in their execution. The only non-worthless thing about them is that they provide a very, very brief description of the locale - before moving on to things that live at the locale that need to be killed for the PCs to gain the powerups.
Don't buy the Planar Handbook.