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Yes, out-of-the-box you can use matchadd().
To add a highlight, eg. for trailing whitespace:
:highlight ExtraWhitespace ctermbg=grey guibg=grey
:call matchadd('ExtraWhitespace', '\s\+$', 11)
To view all matches:
:echo getmatches()
To remove matches use matchdelete(). Eg.:
:call matchdelete(7)
MultipleSearch : Highlight multiple searches at the same time, each with a different color.
http://www.vim.org/scripts/script.php?script_id=479
:Search <pattern1> //will highlight all occurences of <pattern1> in the current buffer.
A subsequent :Search <pattern2> will highlight all occurences of <pattern2> in the current buffer.