There is no limit on tables you can track, so far as I know, from the Pokertracker perspective (PT2 or PT3) - the limits are the number of tables you can open within the software.....
On
Full Tilt, you can open 16 tables at a time. You can collect data (from observed tables) at FT for 16 tables at a time. The "Table Tracker" will show you the stats from your database for, so far as I can see, all active tables within the software - though you are capped to collecting live data from 16 of them.
You can filter the "table tracker" by criteria (number of players, site and buy in). By clicking on a table, you get the data for all players at the table in the box below (see screen print in post 2 for an example - I dont think that what your asking for is directly available (ie flagging certain, active, players based on db criteria) - though cannot see why not and you'd imagine a "plug in" could well become available for that
(there are AHK scripts that search for buddies I think - but you'd need to manually set up a buddy list).
Remember "Table Tracker" is not base functionality in PT3 - it will require a monthly subscription. Also
Full Tilt is the only site so far where you can datamine observed hands (without purchasing extra software). I think you will be able to add microgaming to that list when it becomes supported.