The Guest Era might be something any fan of the OC are familiar with, but what was the real point of it, you may ask yourself after reading or skimping through it?
To that I say, putting aside Mark Martin or the Tom Mcweeney issues, there still was sense of continuity that continued after it was all but declared every issue (with the exception of #27 and #28) from #22 to #44 was no longer canon in the Mirage Continuity.
But wait a minute, if you actually read through some of the issues, you'll realize that some things don't add up or aren't as poignant if you entirely skipped over every issue of this era.
Exhibit A: The River
The River continues Raph's charcter development from RTNC and leads directly into Sons of a Silent Age. If you just skipped over The River, guess what? You just skimped over major development of one of the Turtles. Not to mention the fact that this was the first mention of April and Casey developing feelings for each other; ultimately correlating in City at War.

Exhibit B: Sky Highway
Tatoruzu and Mark Pellegrini I think explained the overall importance of this issue and why skipping it is a bad idea once you get to City at War. This is where we get a taste of how the 57' Chevy is important to understand Casey's charcter in the story and how it'll affect him after it gets stolen in CAW. Without Sky Highway, it just doesn't feel as poignant of a plot device.
Exhibit C: The Ring/ Twilight of the Ring
This story arc feels like an indirect sequel to Sons of a Silent Age (a canon issue). Splinter also mentions the time they traveled to the Cretaceous era with Renet. Splinter tells the Turtles to go on a spiritual quest to set free The Father of Reptiles. This issue is where Don's charcter I think starts to develop a more spiritual conscious similar to Splinter as well, but it sorta contradicts...
Exhibit D: Juliet's Revenge and Halls of Lost Legends
Now, Juliet's Revenge basically ties up the loose ends with Savanti's wife, while Halls of Lost Legends concludes Don's charcter development from The Ring. Although, for my sake, I like to place Halls of Lost Legends before The Ring even if the latter came first.
I think that issues 1-15, 17, 19-21, 24-30, 37, and 42-62 (minus #44) give you the whole story and development of the Turtles (except Mike unfortunately), Splinter, April, and Casey.
So, all that said, I detest that term and think that Peter should've look over some of these other issues more before declaring then "non-canon".