Memory is an intended skill of the game. Players should not use any form of tokens or counters to keep track of anything that is not directly tied to a card effect or game state. Examples of things you can use tokens for: recurring credits, the ice chosen by , and the server chosen by . Examples of things you cannot use tokens for: marking a remote server you've accessed before or keeping track of known access.
I have 2 questions about token usage.
2 - Can the Runner use tokens to represent the number of card draws from R&D since their last multi-access? (eg. Saw no agendas on an run - put 5 counters on the table. Remove one per draw until empty, so that they know the next time they run it'll be a new card.)
In my opinion these situations breach the rule about taking notes, even if they are represented with an in-game token. It is also my opinion that memory is considered a skill in this game, so people who are able to keep track of those 10 Jinteki PE servers deserve a higher win percentage than those who forget which ones were traps that they chose not to trash.