Holodeck

In episode "The Big Goodbye" we are informed that holodecs, are "highly useful for crew training" and "highly enjoyable when used for recreation". However, there are also several other things worth noting - Picard is "not dressed properly" and spot from lipstick holodeck character gave him remained after he exited holodeck, which seems to suggest that, while most of it is illusion created by forcefields and holograms, at least some items are replicated (it is reinforced by "Angel One" when Picard, passing near holodeck, gets hit by snowball throught open doors). Since it is unlikely starship will carry huge amounts of lipstick to be used in replicators as needed, it seems to suggest that at least some level of manipulation on mollecular level can be achieved, if not at atomic/subatomic level.

Death Star II

Before being banned on SDN I have recieved lot of complaints why Federation should not be able to destroy DSII. Microconduits... which we never saw used by Empire. It was also argued that conduit throught which Rebels flew inside was to be removed after construction was finished... which is, to say at least, ridiculous, as seen from following screenshot.

Folks at SDN argue that it was impossible for Rebels to destroy Death Star II after it was completed and that it was main reason why they attacked it. Wrong. Main reason for attack was fact that Emperor was going to be there. Secondary reason was promptly displayed when DSII destroyed cruiser Liberty. Superlaser of DSI was unable to target capital ships.

Also, much simpler solution would be to just put chimney caps. Constructing thousands or millions of micro-exhaust ports with each being over 90 kilometers long (due to zig-zag structure of vents) would be engineering and logistical nightmare, not to mention that construction would be delayed enough to make canon timeframe impossible.

Dreadnought

Dreadnought is nickname Maquis gave to former Cardassian missile. It is self-contained tactical missile. It carries warhead that contains 1000 kg of matter and 1000 kg of antimatter giving it 43-gigaton yield; it is also adaptible, evasive and armed with its own defensive weaponry - in other words, unstoppable. So, warhead itself was big deal, but its other characteristics were what made it such big deal.

Later in episode, we get a look at several other characteristics - it was able to scan and adapt to Starfleet weapons in part of second, rendering them almost completely ineffective.