I'm using Renoise for sequencing - love the old-school tracker workflow! - with a variety of VSTs.
Most of the chiptune-esque tracks use Soraboy, which is a fantastic VST for creating gameboy style sounds.
I'm also a big fan of TAL Noisemaker if I need more typical subtractive synthesis sounds
For soundfonts I use Sforzando and various sample packs from all sorts of places (being careful to check the licence terms, of course). I'm not especially fond of the interface, as it makes basic tasks like browsing through your sample library really clunky, but it's the best solution I've found for now.