Is it ethical/lawful to recolor/scale the logos when importing them to presentation slides to make the logos meet the template standards and fit the theme colors?
Logos are often trademarked, and therefore you are not free to recolor them according to whatever color scheme your template happens to use.
However, many companies and universities do have multiple versions of their logo available, for precisely this reason. You should contact your university's (or organization's) press office (or similar office) to see what is available, before toying with it yourself.
Most companies/institutions guard their branding very carefully. Many companies spend thousands or even millions on developing a brand language, which includes fonts, colors, and other design elements.
I don't know the specifics of the legal ramifications of changing logo colors, but the owners of the logo are sure to be against it.
The following is based on general copyright concepts and should apply to any reasonable copyright laws:
Any logo is created by somebody, be it a professional graphic-design company or the dean’s nephew, and without further ado this person (or company) holds the copyright to that logo. This mostly means that you cannot do certain things with it (or an altered form of it), which usually include dissemination or using it for commercial purposes. Whether using the logo in a presentation shown to a small audience is included in this depends on your country’s copyright and other aspects. Using it in a publication would almost certainly be a breach of copyright, however. Anyway, let’s assume it would not be legal to use the logo for whatever you do.
As it would be pretty pointless, if, e.g., members of a university were not allowed to use its logo (when representing that university), the creator will usually have authorised the university and its members to use the logo – but this authorisation can be bound to conditions. Furthermore the university itself may impose conditions onto its members regarding the usage of the logo. These conditions may include:
Now, if you are lucky, there exists some document which states that members of the university or similar are authorised to use the logo and which contains conditions (if any exist) and requirements of logo usage. Here is an example thanks to Mkennedy.
On the other side of the spectrum, you may have some institute’s logo, which was handrawn by the director’s niece 30 years ago and gone through several iterations of scanning and printing, because the original has been lost. You have no official authorisation to use the logo at all and the legal grey zone you are entering does not change much if you additionally alter the logo (in any remotely respectful manner). It is very likely that nobody will care, let alone sue you.
Where on this spectrum you are is something only you can decide.
Anyway, I would recommend to use such a logo only on one or two slides, so it should not dramatically destroy your colour concept.
Additionally, you might consider adapting your presentation’s colour scheme to the logo’s colour scheme, but beware that the latter is not necessarily a good choice for projectors.
Logotypes are typically covered by what's known as the graphical profile of organisations like companies, universities and indeed even political parties or NGOs.
A graphical profile usually contains things like (but not limited to) color(s), aspect ratio, font(s) and positioning of eventual text elements regarding a logotype in question. Depending on how "complete" or "strict" a graphical profile is, you can do varying degrees of manipulations.
It's typically not an issue to scale the image, given that the aspect ratio, or the width-height proportions are kept as the original. If the organisation in question has put some thought into their graphical profile, they should have the logotype in a vector-based format, which scales up/down without any quality loss.
Keep in mind that scaling up an image is usually not a good idea, if the image is bitmap and not vectorised. It's also good to remember that there might be issues regarding readability, i.e. there might be a limit on how much you can scale down the logotype. Logotypes that have text within the graphics tend to have such limitations. [Keen observer might notice how badly the text renders if one does not pay attention when converting vector graphics to raster graphics]
Finally, even if you are allowed to crop a logo (due use as decoration on the edge of a slide or poster) exactly how you can crop the logo might be defined as well. For instance the logo I linked above has 4 predefined cropped versions, that you are allowed to use. Beyond those you are not allowed to crop/scale/change the logotype in any way.
Just exactly how that might be enforced is a whole different story however.
To clarify the resizing issue discussed in the comments: for any length-based system of preparing a document, the concept of "size" is indeed a valid one.
If the people who provide official University logos have done their job properly, the logo will be available in postscript and/or PDF formats that have a defined size in centimetres. These original dimensions are probably intended for reproduction on A4 paper and in that case should not be changed (in the interest of consistency).
For instance, the .eps logo of my University is defined as being 1.77 cm high. On official, printed A4 letters it is the exact same 1.77 cm in height. In most cases it would be inappropriate to rescale this logo when creating an A4 document. Consistency is good.
As a side note, the concept of measuring Powerpoint slides in pixels is wrong: it's a vectorized document. There are no pixels. I don't have a copy of Microsoft Powerpoint, but Apple Keynote's default slide size is 1024x768 points (not pixels!). 1 pt = 1/72 inch. I suspect Microsoft's system is the same.
A logical method of scaling to different media would be to scale based on the font size of your main body of text. Most A4 documents have 10pt font. So, if you're producing a poster or presentation with a main font size of 24pt, just make the logo 2.4 times wider and taller. This will keep the logo's size in proportion to the rest of the text.