You would be comparing apples with oranges here. Lotus Notes is primarily a mail client, but due to the underlying distributed DB framework there can be any sort of custom solutions on top of it. Alfresco is an ECM system that already has some functionality for knowledge management. You would have to name the specific, Lotus Notes-based solution you want to compare against Alfresco, because a generic comparison is not possible.
One thing you always have to keep in mind though is that Lotus Notes is closed-source, meaning you have less options to customise / more effort to invest into learning the system, and usually less open in terms of interfaces (I haven't checked the latest versions) so whenever you decide it is not a match for you anymore you will have a hard time getting your information out of the system and onto a different one.
