See the shows with more shows last
Shows that have more showings per day are the ones you want to save for later. Because there are more showings of these, it offers the most flexibility in terms of scheduling a show. Voyage of the the Little Mermaid often has around dozens of shows per day as it runs 17 minute shows intermittently throughout the day. On the flip side, Lights, Motors, Action! Extreme Stunt Show is only shown ususally 3 times per day so it will be smart of you to work around the Lights, Motors, Action schedule and when you have some free time later in the day, go see a show like Mermaid.
The less shows per day, the more crowded
This may seem obvious but if a show like Beauty and the Beast or Lights, Motors, Action! Extreme Stunt Show only have 3-5 shows per day, there will be far more people trying to get into these shows than other shows that have lots of showings. Shows that have less than 5 shows per day are the ones you want to show up early for to ensure you do get in because you want to avoid waiting in line for a show and not be able to actually see the show you showed up for.
See the first show
Regardless of how often a show is shown, ideally you should try to see the first performance of the show of the day. In all the research this site has conducted in attendance and in polling the Cast Members who work these shows, the first shows of the day tend to be the least crowded, especially at Lights, Motors, Action! Extreme Stunt Show, the Indiana Jones Epic Stunt Spectacular and Playhouse Disney - Live on Stage. The Studios will hit it's attendance high for the day sometime in the afternoon, so seeing the first show of the day (which usually occurs sometime in the morning) ensures your best chance to see it since you will have the least competition.
To give you an example, at Lights, Motors, Action! Extreme Stunt Show, the first show of the day averages 2500-3000 guests, the second show averages 4500-5000 guests an the third show averages 3500-4000 guests. Clearly the first show will be the best option as you will have the least competition to get in and that has a benefit of you not having to spend a lot of time idly waiting in line.
Prioritize what you want to see
With all of the shows at the Studios, it's hard to see them all and to be honest, most guests don't want to see them all. Many guests with older people in their party are less likely to want to see Playhouse Disney - Live on Stage whereas guests with young children are less interested in seeing a show like Indiana Jones Epic Stunt Spectacular. All that being said, either of those groups may still like to see those shows if they could. It's important to prioritize which shows you absolutely want to see, want to see and are okay with missing. The shows you absolutely you want to see are the ones you work around their schedules to fit them in while other shows may simply be a show you see if time permits.