Hi there!
let's begin with the simple answers
@d-man:
as Chad said - you can accomplish this by using the StealthMode feature.
just hit CTRL+WIN+ALT+PageUp and hide/unhide all icons.
i will eventually implement an option for only stealthen things in one session (right now the state is remembered via registry).
@Demokos:
well, back in the days

i created Min2Tray with the intention of having an icon for every hidden window. but i see a growing demand for an option of just one instance of Min2Tray with a context menu with all minimized windows... i will think about a way to do this. but don't expect anything before v1.7 - no, really!
the idea of yours (grouped windows in menu) is possible, but i don't know how to handle this user-wise (gui, anyone?!?). only guessing a appropriate group by window title will not do. perhaps it will be possible to group windows by their application.
@Chad:
you can alter the hotkey for StealthMode, already! i would say, that is a problem of RTFM

there is no option in the prefs dialog, but you can edit the hotkey to trigger StealthMode in the registry ("Changelog.txt", line 124).
unhiding all windows by only one keypress is unfortunately (at this time) not possible. you can only assign a hotkey per minimized window.
thinking about implementing this one into v1.7...
bringing one particular window to front is not directly possible.
but(!) you could add this window to stay visible to the BossKey list (via context menu of icon of this window when minimized [i know, the handling is a bit crude]). then select Opt-out mode and you are lucky. this will minimize all windows except for the ones on the BossKey list (list can also be inspected via main menu).
*puh* a lot of writing. going into weekend mode now, cheers
Junyx