You can do partial flyspell-mode in a number of different ways. One is to use a multi-mode approach, where you define multiple modes in a single buffer, one of which is a mode to edit comments (for example), in which flyspell-mode is enabled. I used to do this for some programming language, but I can't find the config for it any more, so I guess I don't use that language anymore. Anyhow, see mmm-mode for more info there.
A second alternative is to use `flyspell-prog-mode' (which see) which sets up flyspell mode for certain parts of the buffer, defined in this case by the font face (there are specific faces for strings and comments for most programming language major modes). It uses a predicate call-back function, which can be defined however you want it; I maintain TNT, which is an AIM-mode for Emacs, and we use it like so:
(defun tnt-im-mode-flyspell-verify ()
"This function is used for `flyspell-generic-check-word-p' in TNT."
(not (get-text-property (point) 'read-only)))
(put 'tnt-im-mode 'flyspell-mode-predicate 'tnt-im-mode-flyspell-verify)
(put 'tnt-chat-mode 'flyspell-mode-predicate 'tnt-im-mode-flyspell-verify)
Regarding flyspell vs. speck vs. wcheck -- I've only used flyspell mode. speck seems to be very oriented on what is viewable, which can be fine, but generally I want the whole of whatever document I'm working on to be spell-checked, so I wouldn't want that. wcheck seems to be a generic interface to an external program; I'd guess you're going to have to build up its use yourself. flyspell can be used two different ways: as-you-type, which is how I usually use it, and "batch mode", where a whole region or buffer is checked at once. The former is incredibly fast, and I've never found a reason to look for a better tool. The latter can be a tad slow, especially when there are a lot of misspelled words and the document is large, but I really can't remember waiting more than 15 seconds for it to complete. While watching the screen for 15 seconds and doing nothing can seem like a long time, it's not, really. YMMV, of course.
Bottom line: I'd stick with flyspell-mode, assuming it meets your needs, of course.