On his blog, Pierre-Alain Joye talks about the ext/filter extension and how several developers just choose to "work around" it instead of using its features right out.
On the other hand, the same persons worked around ext/filter with ugly hacks. Edin pointed me to one of these horrible codes in Serendipity, as I saw this code in other applications like flyspray, I think it is time to raise your attention about what to do not do.
The code he's referencing is a snippet that manually filters each of the superglobals to get rid of any problems that might have been put in. He points out two security problems with the code too: only use PHP functions as a fallback when filter isn't available and never use the superglobals directly outside of the filtering.
Stefan Esser has his own comments on the topic too. He votes for the other way around (own functions over filter's methods) and expresses the opinion that the ext/filter extension is a bad idea similar to the impropper use of magic_quotes_gpc.
Pierre has also responded to these comments in an update to how own blog entry. Check it out for the full story...