In python:
>>> import pymongo
>>> import uuid
>>> from pymongo import Connection
>>> c = Connection('localhost', 27017)
>>> db = c.test
>>> db.foo.insert(

{"python": uuid.UUID("aaf4c61d-dcc5-e8a2-dabe-de0f3b482cd9")}

)
ObjectId('4e318fb98f1e81eac4000001')

In java:
UUID id = UUID.fromString("aaf4c61d-dcc5-e8a2-dabe-de0f3b482cd9");
Mongo mongo = new Mongo();
DB db = mongo.getDB("test");
DBObject dbo = new BasicDBObject();
dbo.put("java", id);
db.getCollection("foo").insert(dbo);

Result:
> db.foo.find()

{ "_id" : ObjectId("4e318fb98f1e81eac4000001"), "python" : UUID('aaf4c61ddcc5e8a2dabede0f3b482cd9') } { "_id" : ObjectId("4e318fc12746ac3aa375aee9"), "java" : UUID('a2e8c5dc1dc6f4aad92c483b0fdebeda') }

(yes, with the patch from SERVER-1201 applied)

Java seems to serialize/deserialize the UUIDs as little endian according to BSONEncoder.java, line 354

Changing this would however break a lot of applications out there. However, the python/java incompatibility is really bad, so it should be fixed in my humble opinion...