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I am new to electronics and from what I understand, most protoboards seem to be standardized on a 2.54mm (0.1") pin pitch. I am also aware that there are through-hole components which are manufactured at a 2.5mm pin pitch, namely JST connectors.

Note:

Connector confusion on the internet:

In recent years, it is preferred to use millimeter (mm) instead of inches for pin-to-pin pitch distance. Note: Some 2.50 mm parts are incorrectly sold on the internet as 2.54 mm (0.100 in), and the 1.25 mm parts as 1.27 mm (0.050 in).

I have some JST-XH connectors which fit just fine in a protoboard advertised as having 2.54" pitch spacing and does not feel tight at all; tested on a connector with 8 pins to maximize error.

Should I take any special precaution when mixing 2.5mm specced parts on 2.54mm protoboards or should I expect them all to fit as my JST connector does?

enter image description here

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In general, you should be fine, except possibly on the longest components or connectors. Things only start to "bind" when the accumulated error gets to be on the order of 20% of the pin pitch. That doesn't kick in until you get more than about 12 pins in a row.

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Protoboards are both tolerant of sloppy fits, and are not entirely dependable even on a good day*. I'd say that (A) if it works, you're fine, (B) always check (even if it worked yesterday), and (C) as soon as you know you want to keep that circuit, transfer it to something soldered.

* And note that I'm considered to be insanely willing to use protoboards by some of my circuit design brethren -- protoboards are very limited in what you can trust them for, but within those limits you can do amazing things.

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    \$\begingroup\$ I've included a photo of what I believe is a "protoboard". I think what you're referring to is a breadboard? \$\endgroup\$
    – Zhro
    Oct 13 '18 at 16:06

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