I use a spreadsheet, as it can be sorted easily.  I think I started with a spreadsheet generated through MyHeritage and adapted it for my needs.  In the file, I have one sheet sorted by the name/username and another sorted by chromosome, so I can see matches from MH and FTDNA together.  I also have a sheet listing my strongest DNA matches based on various criteria.  

Ellen

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Ellen Morosoff Pemrick 
Saratoga County, NY

Researching WEISSMAN/VAYSMAN (Ostropol, Ukraine); MOROZ and ESTRIN/ESTERKIN (Shklov & Bykhov, Belarus); LESSER/LESZEROVITZ, MAIMAN, and BARNETT/BEINHART/BERNHART (Lithuania/Latvia); and ROSENSWEIG/ROSENZWEIG, KIRSCHEN, and SCHWARTZ (Botosani, Romania)