I had never noticed that in "Lady in Waiting" before, but that is quite striking. It seems as though some episodes make the time-frame conspicuous when certain "events", such as a funeral or an inquest, which are closely tied to the murder itself, are made set pieces in the story.
One episode I feel portrays the passage of time in an effective way is "How to Dial a Murder", where there's the montage toward the end depicting Columbo working with the dog trainer over an extended period of time. Because of that scene, the whole episode seems richer and more involved to me, portraying Columbo going to great effort to trap the murderer. Of course, most of the episodes already mentioned are still some of my top or second-tier favorites, even with the implausible time-frames.

Often there is no real identifiable timeframe and it's only occasionally when Columbo says something like "Remember that night, a few weeks back..." or similar that you get an idea that's it's been significantly long. There certainly isn't any real feeling of significant time passing.

Exactly, the timeframe is often left very vague. We only see certain events and interactions, with some indeterminate amount of time passing between them. Sometimes it's made explicit that certain events unfolded unseen--for example, when Columbo tells Hassan Sallah that he had tracked down the origin of the money found on Rahman Habib's body (A Case of Immunity), or when he tells Milo Janus that he went to the auto dealership that Janus claimed as his alibi (Exercise in Fatality). We don't see those things happening. Other times it's implied that a lot had to happen off screen, as when the Morris brothers were coached in the show they put on for Marcus Collier (Deadly State of Mind), or when Columbo, Mac, and Kramer worked out all the details of their big "gather all the suspects" presentation (Last Salute to the Commodore). It's just one of those things you're not supposed to give any thought to, because it's really not relevant to the story.

Those are good points about many things happening off-screen. This is a little off-topic, though sort of related, but a complaint Mark Dawidziak had in "The Columbo Phile" was that many of the longer episodes seem padded. With some of the examples he cited (such as "Candidate for Crime" and "An Exercise in Fatality"), I get the impression that the scenes where Columbo is testing theories or obtaining information in a way that may seem mundane and monotonous, present in these two episodes (and usually shown off-screen throughout the series, as you pointed out), are the ones he felt were unnecessary. For me personally, I rather enjoy these scenes; to me, they give a nice insight into how Columbo interacts with people who are more close to his humble standing in life (clerks, gas station attendants etc). I enjoy those references to Columbo's hard work and thoroughness, whether off-screen or on-screen, and for the most part don't feel it's a blight to the show when it is shown. Again, I know that's a little off-topic, but I felt this was a good opportunity to vent about my very slight disagreement with Mark Dawidziak's views on the series.

Watched "Short Fuse" last night and I never realized it was one of those episodes that had a "too much in one day" problem until Anne Francis tells Roddy McDowall that she lied about where she was "last night", which means Columbo has been all the way out to the mountain, up the tram and back to the plant AND heard back the report that points to the explosive inside the card and has now formed his theory about the cigar box AND gets back to the mountain before it's dark. Not likely! I really think these kinds of flaws should have been covered by the script editor better to just change "last night" to "the other day" or something like that.