1. Are there differences between scripts made for POL 095 - 098. Means: is it a good idea to make an extra category for every POL version?
Yes there are major differences between pre-POL 0.96 and POL 0.96 and later. There are less major differences between POL 0.96 to the current stable "official" release, POL 0.98. Almost any script for POL 0.95 and earlier needs to be updated to be compatible with POL 0.96 and beyond Many of those scripts will not compile properly under post 0.95 POL. Differences in later POL versions (0.96 to 0.99 (the current version under development)) involve less severe changes and most likely will compile. Certainly all POL 0.96 scripts are upwards compatible with the Core as it currently stands. The same is not true for pre-0.96 scripts. To answer your question, yes, if you are going to allow POL 0.95 scripts to be uploaded by your users, you should have different areas for them. One of the major differences between POL 0.95 and later versions is multiple map support. POL 0.95 only supported one map.
2. Is there a way you are categorizing your scripts? I know it from sphere, there you have categories like Events, Functions, Items, Script pack etc.
Not so much here on the polserver.com site. They do have a section for Complete Worlds and then a section for all other script contributions. I have been around since the old Yahoo! POL Group days and over there they had more categories. Here are some examples from what I remember:
Complete Worlds: I can't remember if they had this category on the Groups site but this should be one of your categories. This would contain complete, ready to compile, full working shards. Preferably, if they used custom maps those would be included. The reason I suggest including the maps is that many of these worlds have special starting areas for players as well. If I were setting this up I would also ask that the contributors to this category include the world data files that contain the items for a "virgin" installation of the world. By "virgin" I mean items that are placed by the decorators of the world prior to any player placed items. Again my reasoning here is that many shards have custom gateways for selecting classes and races etc. If a contributor cannot or will not provide the items file then they should provide instructions for setting up a class/race starting area if their scriptset has one. Yeah, I know. I'm picky.
Packages: These are complete packages that can be placed in the "pkg" directory of your POL server. Packages can be a set of utilities such as gump utilities, control systems such as weather or day/night control, in game systems such as magic systems or crafting systems or AI systems.
I think they even had an "Experimental" sub category for packages.
Commands: These are <dot> commands that are placed in the appropriate command directory depending on the command level they are intended for. An example might be a .online command that would return a list of online players. These could also include "console" commands that would only be accessible from the POL server console.
Includes: Include files might contain some function or functions that would be usable in many different scripts. An example would be a set of functions that would allow a script to locate and have access to a players bank.
Configuration files: These are files that contain formatted plain text data. An example might be a file that contains a list of all the NPCs that are in the client files.
Miscellaneous: I don't think they had this category. I'm offering it as a suggestion. This is the catch-all category for scripts or files that don't fit in any of the other categories.
I like having the script contribution area broken up into various categories.
One other consideration to think about is a design area. This might include map design tips, ideas and tutorials for creating game art, game mechanics, etc.
I hope this is helpful. Feel free to PM me if you need anything. I do have a few utilities and scripts and such that I have collected over the past 12 years. I would be happy to provide those that are or were publicly available to your site.