GEDMatch—free utility site for comparing autosomal DNA files from most testing companies, also comparing GEDCOM files, many useful tools.
DNAGedcom—site created to help users quickly analyze data from FTDNA, 23andMe, GEDMatch, and MyHeritage. There are tools for comparing GEDCOMs, grouping DNA data together in a visually appealing manner, and triangulating and comparing segments chromosome by chromosome without a spreadsheet.
Genealogical DNA Analysis Tool—free desktop tool for managing autosomal DNA comparisons and identifying common ancestors.
Charting Companion from Progeny Genealogy—desktop application (available for Windows only) for creating charts including x-chromosome charts. Cost: about $35.
DNAPainter —user-friendly online tool for mapping chromosome segments to ancestors. Also provides research tools for analyzing cM shared with matches.