Both MongoDB and CouchDB are document oriented databases with JSON style object data storage.  They have their pros and cons in different situations.

1) Map Reduce

Mongo uses map reduce for data processing jobs, Couch uses map reduce for build all views.

2) Atomicity

Both support concurrent modifications of single documents. Both forego complex transactions involving large numbers of objects.

3) Interface

Couch uses REST as its interface to the database. Mongo relies on language specific database drivers.

4) Query Expression

Couch uses index building schemes to generate indexes those support particular queries. Mongo uses traditional dynamic queries and query optimizer to determine whether index exists or not.

5) Horizontal Scalability

Couch uses replication as a way to scale, instead Mongo uses sharding as a way to scale that is similar to Google’s BigTable.

6) Storage strategy

Couch MVCC based, Mongo uses traditional approach and updates an object in place when possible.

Use cases

Couch is very good for certain classes of problems: problems which need intense versioning; problems with offline databases that resync later; problems where you want a large amount of master-master replication happening.

Mongo is very good for different kind of problems:

problems requiring high update rates of objects are a great fit; compaction is not necessary.

Mongo is more oriented towards master/slave and auto failover configurations than to complex master-master setups.
With MongoDB you should see high write performance, especially for updates.