Well, here's two longstanding ones that are still unfixed in the 4.9.1 beta...

#1 -- Files with the "File Corrupt" or "Waiting in Line" status seem to stop other files from downloading. If I have a corrupt file I haven't removed and four files waiting in line, and have the default five download slots, nothing will download -- everything will stay queued. Only "connecting..." and "downloading" items should count towards those slots.

#2 -- Typing underscores into the search box produces a beep instead of inserting an underscore. Given how common underscores are in filenames, and therefore how useful they can be in narrowing a search for specific files, this is a serious problem. The search box should accept any character that's legal in filenames -- on any filesystem. So, just about any printable character whatever.

Also, searching still makes the GUI freeze for several seconds. It has done since version 3.something. If it's the first search in a while. Sometimes if you launch several searches, the GUI freezes only after you hit enter for the first one.